I think you should tone down the "abandoned building" idea just a tad. It's redundant with units requiring resources, and it provides a double penalty in the event you lose access to something in the event that the building provides some other benefit.
In a recent game, I lost access to Reagents because the only civ who had any declared war on me. It was bad enough not being able to make any mages, but losing the science output on my wizard's towers added on would have been a harsh blow.
What it amounts to, as far as I can see, is requiring one resource to make another resource, and basing a unit's availability upon that. But it sounds like alot of extra work when gameplay won't be affected that much or only negatively, IMO.