Added a modified zkcli.bat script to overlay, 

this will be available after installation to interact with ZooKeeper.

I do not have a linux host here to test with a .sh script, but it should be easy to port. 

There are examples for invocation in the script. Unfortunately I made our deployment in powershell instead of using the necessary time to learn how to do it in the izpack installer. The same powershell script also downloads and installs ZooKeeper separately. if you like, @janhoy , I can give you access to that repo and you can port it to izpack. I will probably not have the time to do it. (And you talked about fixing the chicken-egg problem of solr/zk in solr itself, so I've been waiting for that instead of fixing this properly)

Adding two lines in the izpack installer after the service starts up with
$openEspInstallationDir\cloud-scripts\zkcli.bat -cmd upconfig -zkhost ${zooKeeperHost}:${zooKeeperPort} -confdir ${openEspInstallationDir}\conf\solr\collection1\conf -confname conf1
and 
$openEspInstallationDir\cloud-scripts\zkcli.bat -cmd linkconfig -zkhost ${zooKeeperHost}:${zooKeeperPort} -collection collection1 -confname conf1"
should fix it. Solr might have to be restarted for it to pick up the new config in zk.