As long as you aren’t disturbing the animals any more than you would be on foot, I’d say have at it. There’s some contexts where a drone is worse than a person on foot (like the idiot who crashed one into a least tern nesting site here in southern California and caused thousands of terns to abandon their nest, or people who fly them over nesting snowy plovers and flush them). In general I’d say be careful with birds in particular, and don’t fly near any nesting ones for obvious reasons.
For stuff like scouting out habitat like you said or observing plants on cliffs, that sounds like an excellent idea!
Have fun with the legality of flying, though… I essentially gave up on using my drone years ago because the regulations are all over the place and constantly changing. It was incredibly frustrating that I could really never be sure I was actually obeying the law in any given place, and the outlandish general public opinion that goes between “don’t fly in a city because you’re spying on me” (when that could be done far more effectively with a cell phone that you wouldn’t even question?) to “don’t fly in the middle of nowhere because you’re disturbing the tranquility” (but OHVs and cars are ok?) didn’t help.