That will require some investigation into the version service. It could be as simple as configuration or it could require a fairly substantial piece of rework to version the child assocs.
I don't think there is an easy answer. AVM does have its good points!
My best guess would be to add a custom behavior on the event "onCreateVersion" that bubbles up to the parent folders. This could take care of the data part of the problem but I don't really know how it would fit in the UI.