Crouching Tiger Hidden Dragon and Joint Security Area both feature something kinda like this, but the "villain" is presented sympathetically from the start, and both sides develop instead of just having the antagonist change for the sake of the protagonist. Decision to Leave might be closer, but I get the feeling you're looking for a movie that might involve political conflict and that movie is focused on few interpersonal conflicts.
Crouching Tiger Hidden Dragon and Joint Security Area both feature something kinda like this, but the "villain" is presented sympathetically from the start, and both sides develop instead of just having the antagonist change for the sake of the protagonist. Decision to Leave might be closer, but I get the feeling you're looking for a movie that might involve political conflict and that movie is focused on few interpersonal conflicts.
Yeah Avatar is an obvious example too, but the blue guys are sympathetic almost immediately.