[Galaxy S II Android Development] mialwe:
@OP, sorry for OT but I want to answer this.

Just have tested this with a self-deodexed version of a slimmed down 4.1.2, currently using only 230Mb in /preload, nothing besides symlinks in /system/app. I needed only one placeholder (e.g. dummy.txt) in the CWM zip for keeping the otherwise empty app directory in /system and even this directory could be created via the CWM script on the fly.

I did not understand why placeholders are needed for each apk as symlinks can be created via the CWM updater script.

The needed lines can be quickly put together via a good text editor and/or bash, my resulting and working updater zip looks like this right now (flashed, booted, works). This wipes cache/dalvik cache, clears /preload/.../app, /system/app and /system/framework, extracts the deodexed packages, sets permissions and creates the symlinks:

ui_print("");
ui_print("Mounting partitions...");
run_program("/sbin/mount", "/dev/block/mmcblk0p9", "/system");
run_program("/sbin/mount", "/dev/block/mmcblk0p10", "/data");
run_program("/sbin/mount", "/dev/block/mmcblk0p12", "/preload");
mount("ext4", "EMMC", "/dev/block/mmcblk0p7", "/cache");
ui_print("Cleaning caches...");
delete_recursive("/cache");
delete_recursive("/data/dalvik-cache");
show_progress(0.500000, 80);
ui_print("Removing preload apks, framework and /system/apps...");
delete_recursive("/system/app");
delete_recursive("/system/framework");
delete_recursive("/preload/symlink/system/app");
ui_print("Extracting...");
package_extract_dir("preload", "/preload");
package_extract_dir("system", "/system");
ui_print("Setting permissions...");
set_perm_recursive(0, 0, 0755, 0644, "/system/framework");
set_perm_recursive(0, 0, 0755, 0644, "/system/app");
set_perm_recursive(0, 0, 0755, 0644, "/preload/symlink/system/app");
ui_print("Creating symlinks...");
symlink("/preload/symlink/system/app/AllshareMediaServer.apk","/system/app/AllshareMediaServer.apk");
symlink("/preload/symlink/system/app/AllSharePlay.apk","/system/app/AllSharePlay.apk");
symlink("/preload/symlink/system/app/AllshareService.apk","/system/app/AllshareService.apk");
symlink("/preload/symlink/system/app/ApplicationsProvider.apk","/system/app/ApplicationsProvider.apk");
symlink("/preload/symlink/system/app/BackupRestoreConfirmation.apk","/system/app/BackupRestoreConfirmation.apk");
symlink("/preload/symlink/system/app/BadgeProvider.apk","/system/app/BadgeProvider.apk");
symlink("/preload/symlink/system/app/BCService.apk","/system/app/BCService.apk");
symlink("/preload/symlink/system/app/BluetoothAvrcp.apk","/system/app/BluetoothAvrcp.apk");
symlink("/preload/symlink/system/app/BluetoothMap.apk","/system/app/BluetoothMap.apk");
symlink("/preload/symlink/system/app/BluetoothTest.apk","/system/app/BluetoothTest.apk");
symlink("/preload/symlink/system/app/CapabilityManagerService.apk","/system/app/CapabilityManagerService.apk");
symlink("/preload/symlink/system/app/CertInstaller.apk","/system/app/CertInstaller.apk");
symlink("/preload/symlink/system/app/ChromeBookmarksSyncAdapter.apk","/system/app/ChromeBookmarksSyncAdapter.apk");
symlink("/preload/symlink/system/app/ClipboardSaveService.apk","/system/app/ClipboardSaveService.apk");
symlink("/preload/symlink/system/app/ClockPackage.apk","/system/app/ClockPackage.apk");
symlink("/preload/symlink/system/app/ContextAwareService.apk","/system/app/ContextAwareService.apk");
symlink("/preload/symlink/system/app/CSC.apk","/system/app/CSC.apk");
symlink("/preload/symlink/system/app/DataCreate_U1_EUR_OPEN.apk","/system/app/DataCreate_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/DefaultContainerService.apk","/system/app/DefaultContainerService.apk");
symlink("/preload/symlink/system/app/Divx.apk","/system/app/Divx.apk");
symlink("/preload/symlink/system/app/DrmProvider.apk","/system/app/DrmProvider.apk");
symlink("/preload/symlink/system/app/DSMForwarding.apk","/system/app/DSMForwarding.apk");
symlink("/preload/symlink/system/app/DSMLawmo.apk","/system/app/DSMLawmo.apk");
symlink("/preload/symlink/system/app/EdmSysScopeService.apk","/system/app/EdmSysScopeService.apk");
symlink("/preload/symlink/system/app/EdmVpnServices.apk","/system/app/EdmVpnServices.apk");
symlink("/preload/symlink/system/app/EnterprisePermissions.apk","/system/app/EnterprisePermissions.apk");
symlink("/preload/symlink/system/app/FaceLock.apk","/system/app/FaceLock.apk");
symlink("/preload/symlink/system/app/FactoryTest_U1_EUR_OPEN.apk","/system/app/FactoryTest_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/FmmDM.apk","/system/app/FmmDM.apk");
symlink("/preload/symlink/system/app/FmmDS.apk","/system/app/FmmDS.apk");
symlink("/preload/symlink/system/app/FmRadio.apk","/system/app/FmRadio.apk");
symlink("/preload/symlink/system/app/GameHub_2.0_ICS_WVGA_ngmoco.apk","/system/app/GameHub_2.0_ICS_WVGA_ngmoco.apk");
symlink("/preload/symlink/system/app/Gmail.apk","/system/app/Gmail.apk");
symlink("/preload/symlink/system/app/GmsCore.apk","/system/app/GmsCore.apk");
symlink("/preload/symlink/system/app/GMS_Maps.apk","/system/app/GMS_Maps.apk");
symlink("/preload/symlink/system/app/GoogleBackupTransport.apk","/system/app/GoogleBackupTransport.apk");
symlink("/preload/symlink/system/app/GoogleCalendarSyncAdapter.apk","/system/app/GoogleCalendarSyncAdapter.apk");
symlink("/preload/symlink/system/app/GoogleContactsSyncAdapter.apk","/system/app/GoogleContactsSyncAdapter.apk");
symlink("/preload/symlink/system/app/GoogleFeedback.apk","/system/app/GoogleFeedback.apk");
symlink("/preload/symlink/system/app/GoogleLoginService.apk","/system/app/GoogleLoginService.apk");
symlink("/preload/symlink/system/app/GooglePartnerSetup.apk","/system/app/GooglePartnerSetup.apk");
symlink("/preload/symlink/system/app/GoogleSearchWidget.apk","/system/app/GoogleSearchWidget.apk");
symlink("/preload/symlink/system/app/GoogleServicesFramework.apk","/system/app/GoogleServicesFramework.apk");
symlink("/preload/symlink/system/app/GoogleTTS.apk","/system/app/GoogleTTS.apk");
symlink("/preload/symlink/system/app/InputDevices.apk","/system/app/InputDevices.apk");
symlink("/preload/symlink/system/app/InputEventApp_U1_EUR_OPEN.apk","/system/app/InputEventApp_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/JobManager.apk","/system/app/JobManager.apk");
symlink("/preload/symlink/system/app/KeyChain.apk","/system/app/KeyChain.apk");
symlink("/preload/symlink/system/app/Keystring_factory_JBUP.apk","/system/app/Keystring_factory_JBUP.apk");
symlink("/preload/symlink/system/app/LogsProvider.apk","/system/app/LogsProvider.apk");
symlink("/preload/symlink/system/app/MediaUploader.apk","/system/app/MediaUploader.apk");
symlink("/preload/symlink/system/app/minimode-res.apk","/system/app/minimode-res.apk");
symlink("/preload/symlink/system/app/MobilePrint.apk","/system/app/MobilePrint.apk");
symlink("/preload/symlink/system/app/MobileTrackerEngineTwo.apk","/system/app/MobileTrackerEngineTwo.apk");
symlink("/preload/symlink/system/app/MtpApplication.apk","/system/app/MtpApplication.apk");
symlink("/preload/symlink/system/app/MusicFX.apk","/system/app/MusicFX.apk");
symlink("/preload/symlink/system/app/MusicPlayer.apk","/system/app/MusicPlayer.apk");
symlink("/preload/symlink/system/app/NetworkLocation.apk","/system/app/NetworkLocation.apk");
symlink("/preload/symlink/system/app/OmaCP.apk","/system/app/OmaCP.apk");
symlink("/preload/symlink/system/app/OmaDrmPopup.apk","/system/app/OmaDrmPopup.apk");
symlink("/preload/symlink/system/app/PackageInstaller.apk","/system/app/PackageInstaller.apk");
symlink("/preload/symlink/system/app/PanningTryActually.apk","/system/app/PanningTryActually.apk");
symlink("/preload/symlink/system/app/PCWClientS.apk","/system/app/PCWClientS.apk");
symlink("/preload/symlink/system/app/PhoneErrService.apk","/system/app/PhoneErrService.apk");
symlink("/preload/symlink/system/app/Phonesky.apk","/system/app/Phonesky.apk");
symlink("/preload/symlink/system/app/Phone_Util_U1_EUR_OPEN.apk","/system/app/Phone_Util_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/PopupuiReceiver.apk","/system/app/PopupuiReceiver.apk");
symlink("/preload/symlink/system/app/Preconfig.apk","/system/app/Preconfig.apk");
symlink("/preload/symlink/system/app/PreloadInstaller.apk","/system/app/PreloadInstaller.apk");
symlink("/preload/symlink/system/app/SamsungCamera.apk","/system/app/SamsungCamera.apk");
symlink("/preload/symlink/system/app/SamsungIME.apk","/system/app/SamsungIME.apk");
symlink("/preload/symlink/system/app/SamsungTTS.apk","/system/app/SamsungTTS.apk");
symlink("/preload/symlink/system/app/SamsungWidget_ProgramMonitor.apk","/system/app/SamsungWidget_ProgramMonitor.apk");
symlink("/preload/symlink/system/app/SecBluetooth.apk","/system/app/SecBluetooth.apk");
symlink("/preload/symlink/system/app/SecBrowser.apk","/system/app/SecBrowser.apk");
symlink("/preload/symlink/system/app/SecCalculator2.apk","/system/app/SecCalculator2.apk");
symlink("/preload/symlink/system/app/SecCalendar.apk","/system/app/SecCalendar.apk");
symlink("/preload/symlink/system/app/SecCalendarProvider.apk","/system/app/SecCalendarProvider.apk");
symlink("/preload/symlink/system/app/SecContacts.apk","/system/app/SecContacts.apk");
symlink("/preload/symlink/system/app/SecContactsProvider.apk","/system/app/SecContactsProvider.apk");
symlink("/preload/symlink/system/app/SecDownloadProvider.apk","/system/app/SecDownloadProvider.apk");
symlink("/preload/symlink/system/app/SecDownloadProviderUi.apk","/system/app/SecDownloadProviderUi.apk");
symlink("/preload/symlink/system/app/SecEmail.apk","/system/app/SecEmail.apk");
symlink("/preload/symlink/system/app/SecExchange.apk","/system/app/SecExchange.apk");
symlink("/preload/symlink/system/app/SecFactoryPhoneTest.apk","/system/app/SecFactoryPhoneTest.apk");
symlink("/preload/symlink/system/app/SecFileShareClient.apk","/system/app/SecFileShareClient.apk");
symlink("/preload/symlink/system/app/SecFileShareServer.apk","/system/app/SecFileShareServer.apk");
symlink("/preload/symlink/system/app/SecGallery2.apk","/system/app/SecGallery2.apk");
symlink("/preload/symlink/system/app/SecHTMLViewer.apk","/system/app/SecHTMLViewer.apk");
symlink("/preload/symlink/system/app/SecLauncher2.apk","/system/app/SecLauncher2.apk");
symlink("/preload/symlink/system/app/SecMediaProvider.apk","/system/app/SecMediaProvider.apk");
symlink("/preload/symlink/system/app/SecMms.apk","/system/app/SecMms.apk");
symlink("/preload/symlink/system/app/SecOmaDownloadProvider.apk","/system/app/SecOmaDownloadProvider.apk");
symlink("/preload/symlink/system/app/SecPhone.apk","/system/app/SecPhone.apk");
symlink("/preload/symlink/system/app/SecSettings.apk","/system/app/SecSettings.apk");
symlink("/preload/symlink/system/app/SecSettingsProvider.apk","/system/app/SecSettingsProvider.apk");
symlink("/preload/symlink/system/app/SecSetupWizard.apk","/system/app/SecSetupWizard.apk");
symlink("/preload/symlink/system/app/SecTelephonyProvider.apk","/system/app/SecTelephonyProvider.apk");
symlink("/preload/symlink/system/app/SecurityProvider.apk","/system/app/SecurityProvider.apk");
symlink("/preload/symlink/system/app/SecWallpaperChooser.apk","/system/app/SecWallpaperChooser.apk");
symlink("/preload/symlink/system/app/SelfTestMode_U1_EUR_OPEN.apk","/system/app/SelfTestMode_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/SerialNumberLabelIndicator_JBUP.apk","/system/app/SerialNumberLabelIndicator_JBUP.apk");
symlink("/preload/symlink/system/app/serviceModeApp_U1_EUR_OPEN.apk","/system/app/serviceModeApp_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/SetupWizard.apk","/system/app/SetupWizard.apk");
symlink("/preload/symlink/system/app/SharedStorageBackup.apk","/system/app/SharedStorageBackup.apk");
symlink("/preload/symlink/system/app/shutdown_JBUP.apk","/system/app/shutdown_JBUP.apk");
symlink("/preload/symlink/system/app/SmartcardService.apk","/system/app/SmartcardService.apk");
symlink("/preload/symlink/system/app/SPPPushClient_Prod.apk","/system/app/SPPPushClient_Prod.apk");
symlink("/preload/symlink/system/app/Stk.apk","/system/app/Stk.apk");
symlink("/preload/symlink/system/app/Superuser.apk","/system/app/Superuser.apk");
symlink("/preload/symlink/system/app/SysScope.apk","/system/app/SysScope.apk");
symlink("/preload/symlink/system/app/SystemInfo_U1_EUR_OPEN.apk","/system/app/SystemInfo_U1_EUR_OPEN.apk");
symlink("/preload/symlink/system/app/SystemUI.apk","/system/app/SystemUI.apk");
symlink("/preload/symlink/system/app/talkback.apk","/system/app/talkback.apk");
symlink("/preload/symlink/system/app/TasksProvider.apk","/system/app/TasksProvider.apk");
symlink("/preload/symlink/system/app/TrimApp_phone.apk","/system/app/TrimApp_phone.apk");
symlink("/preload/symlink/system/app/TwDVFSApp.apk","/system/app/TwDVFSApp.apk");
symlink("/preload/symlink/system/app/UserDictionaryProvider.apk","/system/app/UserDictionaryProvider.apk");
symlink("/preload/symlink/system/app/VideoPlayer.apk","/system/app/VideoPlayer.apk");
symlink("/preload/symlink/system/app/VoiceRecorder.apk","/system/app/VoiceRecorder.apk");
symlink("/preload/symlink/system/app/VoiceSearchStub.apk","/system/app/VoiceSearchStub.apk");
symlink("/preload/symlink/system/app/voice_talk_U1.apk","/system/app/voice_talk_U1.apk");
symlink("/preload/symlink/system/app/VpnDialogs.apk","/system/app/VpnDialogs.apk");
symlink("/preload/symlink/system/app/WAPPushManager.apk","/system/app/WAPPushManager.apk");
symlink("/preload/symlink/system/app/wssyncmlnps.apk","/system/app/wssyncmlnps.apk");
ui_print("Unmounting...");
run_program("/sbin/umount", "/system");
run_program("/sbin/umount", "/data");
run_program("/sbin/umount", "/preload");
run_program("/sbin/umount", "/cache");
ui_print("Done. Please reboot.");

Relevant partitons/available space:

~ # df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/block/mmcblk0p9 516040 378372 137668 73% /system
/dev/block/mmcblk0p12
516040 230592 285448 45% /preload