Have you played Obsidians other works? They love deconstructing tropes. It’s what they’re known for, aside from top-tier writing and being screwed over by their publishers.

• Pillars of Eternity has a cleric party member who’s a bitter old man that openly hates his own god.
• Alpha Protocol is a clusterfuck of factions allying with and betraying each other, and remains the single most reactive RPG ever made (nearly every choice has consequences, sometimes thirty hours later). It’s hard to recommend though because the gameplay is terrible and it’s probably their buggiest game (it was rushed out the door by Sega, who refused to pay for post-release patches).
• Tyranny puts you into the shoes of an executive officer in the Evil Overlord’s army after they’ve already won. I haven’t played it but I’ve only heard good things.
• And of course New Vegas brought the Fallout series back to its morally gray roots by having all sides be terrible, but giving compelling practical (if not moral) reasons to side with them anyway.