I dunno about figuring it all out for you but here's what I think:
I agree that enforcing uniqueness on file extensions is the right thing to do for now.
For expediency's sake I suggest creating a basic list of extensions, just the ones that seem the most common, and let people add more as they need them. No duplicate mime-types in the list, so you don't have to handle that case.
This leaves the work of fixing it the rest of the way to the next person who really needs it to work "right", which might be kind of unfair, but that *is* the way open source works...
