Avatar and Animal Kingdom have consistent underlying values systems and thus arrive at a lot of the same conclusions. It's clear that the "intrinsic value of nature" is a premise or foundational principle that both share. From that overarching theme comes the specific messages of the stories told in Animal Kingdom's attractions and in Avatar's narrative that relate back to that original premise. One of the themes that's often emphasized in the park is conservation, but it's not the only one and it isn't the foundational "central message that ties everything together." (The idea that it's fundamentally just about animals or how they're meaningful to us, though, is a misinterpretation considering what the park's lead imagineer has said and how that's evidenced in the park.)Conservation is an important message in several of the attractions, but it is not the central message that ties everything together.
So the "intrinsic value of nature" isn't just a point of conflict or symbol - it's the reason why the film exalts the indigenous as greater protectors of the planet. In any case, perfect alignment with a park's central message isn't absolutely necessary and very rarely is the case with Disney, but in this case it comes very close: evidence for the similarities are plentiful and obvious. On the other hand, the evidence for what Cars, The Little Mermaid, and Monsters, Inc. have to do with California is more tenuous and ironically provokes fewer complaints here, but Avatar warrants a scathing editorial and tons of comments objecting to it.