1) You know TV tropes had a debate about whether it was right to relocate the Ba'ku or not and someone mentioned something I found interesting, which is that there was nothing in the film to indicate that the Ba'ku were theses selfish bastards like some fans seem to think.
2) I find it disturbing that some fans not only think that every planet in a certain area belongs to the federation regardless of if the people living their have joined it or not or are not living in a federation colony and that they seem to think this doesn't count as imperialism in any way and that it is in fact a good thing.
The other glaring hole is that it's a big planet! The baku have one village, ON A WHOLE PLANET. Just bring sick people or people in need of the properties of the planet and stick them on the other side of the world, really.
Honestly I get the impression that the Ba'ku probably wouldn't have cared as long as you weren't building the medical facility in the valley they lived in and its not like there weren't other nice placed to put it.