Why is Ian working for a company that totally goes against his beliefs???

If I heard correctly while watching the movie, I think Ian was just spying on them or investigating them and pretending to play along while spying/investigating/being undercover. There is a point when Ellie and Alan show up, Ian pulls Ellie aside and starts telling her all this stuff in pretty much a whisper. Someone is making coffee for Ellie, Alan, and Ian and Ian and Ellie are trying to quickly talk (and whisper, although we the audience can still hear what they are saying) while the coffee blender is making all kinds of noise so the surveillance cameras can't pick up what they are saying. Everything Ian tells Ellie while the blender is going is all the info he learned while "working" there.

Ellie, I think acts the way she does is because her kids are off to college now and she feels free and can get back to work without having to worry about her kids too much or being home with them aka be a full-time mom. She even says in the movie that her kids are in college and she feels like she has all this freedom/extra time to do whatever she wants now. So she is probably on some freedom high throughout the movie and it's causing her to act the way she is.

Morals and ethics are all well and good, but Ian had five kids, probably from five different women. Dude probably went broke paying child support and putting them through college. Not to mention he's probably paying alimony to Julianne Moore.

He's counting on that Biocen money, plus the lawsuit settlement from when the dinosaurs inevitably escape(they always do).

Life ... uh ... finds a way