in the case of limiting aqueducts and hospitals, there's still the issue of placing cities on rivers. it would be difficult in some areas, and unrealistic in general, to not place cities on rivers - which give a "free" aqueduct.
i like the idea of using limiting (ie -1) resources that would appear from a tech only indigenous can get. however, i dont believe there's a way to layer those resources with the existing bonuses. this is important as any city will (naturally) use its best tiles for production. even if all other tiles have negatives, the bonus tiles in the territory will be enough to push growth forward to some degree. this might still work with some creative map fiddling, but i'm doubtful.
that said, with a bunch of "never build" instructions on the indigenous peoples, you may just find that further tweaking is not necessary... dont know if this is true, but it would be easy to test once you get to that point.
@camber - i'm diggin the idea of 4 and 4.
EW