The reason Indy conflicts with the themes of DAK isn't because he can't explore man's relationship with nature. Actually, archaeologists study that kind of thing all the time. Man's relationship with nature isn't a theme though. It's a topic. Themes are how an author approaches a topic and what they have to say about it. Stuff like, nature has intrinsic value, and you should want to preserve it. That's the stuff an Indy ride needs to get right. Just being about man & nature won't make the ride fit in Animal Kingdom.
You've got to get the themes right and Indy simply does not care about any of DAK's themes. If Indy studies man's relationship to nature, it will be in a way that is purely anthropocentric, because he's an anthropologist, and he would only study animals for the extrinsic reasons of how they relate to humans, not for their own intrinsic worth. And if that's the case, then the ride will struggle to deliver a message of conservation, which again, is not really a message Indiana Jones lends itself to in any way.