Revert "Performance tweaks."

Reverting @jwage's performance tweaks from #652.

This seems to cause some issues with embedded object persistence and memory leaks. See:

 * #671: Merging and persisting a document containing embedded documents cause embedded documents to be forgotten
 * #679: Embedded Documents not persisted when using APC as cache
 * #681: ReferenceMany: persist references does not work anymore
 * #678: Modification(s) in commit cc4960a cause a memory leak when persisting/updating a document