I don't see why it wouldn't hurt just to properly shield end end of each wire, then stuff them under the carpet. That way you or the next owner has an easy way of hooking up a sub and amp in the future.
Sorry if this doesn't help. It's' probably what I would do. Other than that, uninstalling should really be as simple as disconnecting all the cables and pulling them out from under the carpeting. Is it a stock or aftermarket deck?