It bothers me a little, but not much. It's an expansion in a park that REALLY needs an expansion, but I really would have preferred Australia, and I think Avatar looks kind of silly.
On the other hand, even though it's not a Disney movie, I still think it fits in with Animal Kingdom in that it fits in with the "imaginary creatures" idea. When Animal Kingdom was built, it was promoted as a place that focused on animals, both past (extinct animals such as dinosauars), present (lions, gorrillas, etc) and mythical. For the mythical part, we all know that Beastly Kingdom is what was planned, but it never happened for various reasons. And I read that many of the designers of BK went on to work for Universal and incorporate their ideas into the lost continent section of Universal. And for that reason, Disney decided that they could never built Beastly Kingdom because, even though it was their idea first, it would appear as a knock off of Universal's Lost Continent. So, since WDW can't do Beastly Kingdom, they picked AvatarLand as their place to showcase mythical creatures. So for that reason, I think it fits.
And as others have mentioned, there are plenty of non Disney franchises featured at DHS: Star Wars, Indiana Jones and Muppets. Sure, I know Disney actually purchased the muppets eventually, but since they were not affiliated with Disney whatsoever for so long (as opposed to Pixar, which was always tied with Disney even before the official acquisition), to me, they are non-Disney even though they are actually owned by Disney now.