The thing about the good/bad ending is that the don't automatically slam you with the bad ending if you kill a single person. I'm shit at stealth games and I got discovered a lot, forcing me to kill dozens of guards before I finally got to the final level, but in-between killing I used as many non-lethal takeouts and tranquilizer darts as possible and apparently the game noticed and cut me some slack, because despite of the dozens of guards I had killed, it acknowledged that I was at least trying to keep the body count to a minimal, even if I kept fucking that up, and gave me the good ending. In other words the game gives you some wiggle room and if you make an active effort to not kill everyone you see than getting the good ending should be pretty easy.
I'll admit that the story was rather disappointing though.