The big problem with the ending was giving you a choice. It would have made more sense if they'd treated the act of playing game as the choice itself, meaning that by playing all the way through you've already made the choice to go down that dark path of violence and death.
Never mind that the "bad" ending is probably the worst thing ever. I mean, honestly, Ubisoft.

And they really should have gone full crazy, instead of just giving you a few glimpses of it during those awesome drug sequences. More Apocalypse Now, less generic FPS missions.