I like the idea, mainly because I spent most of Avatar rooting for Quarditch (easily the biggest badass in the last decade of cinema), but it seems like there's another way to do it that might have a bit more power;

Why not have them both be "right," according to their own value systems anyway, and then have the end-game slideshow in both branches tell the player the story of what they did from the perspective of the other side?

In terms of workload, it seems minimal; from a story perspective you already need both sides to have sympathetic and unsavory elements anyway, while from a design perspective all you need to add is a second set of narration captions for the slideshow contingent on which side the player supported.

And in terms of appeal, it certainly seems more engaging than most AAA games. Spec Ops: the Line proved that players are masochists and that throwing guilt trips at them is a great way to get sales and good reviews, while Mass Effect 3's failure shows that genuine choice in endings is pretty important for a game built on moral choice.