Yahtzee pretty much echoed my thoughts about part of this... the moral choice system. One of the reasons why I pretty much stopped messing with it and feel I wasted my money is because to play as a good guy, you pretty much have to neglect 90% of the tools the game gives you. Your pretty much handed a bunch of toys and then told you'll be punished if you play with them. Of course it's also true that if you take the "stealth, meh" approach and just kill everyone and everything in your way, the game becomes a heck of a lot easier, and perhaps more realistic given the overall situation and the supposed capabilities of our protaganist.
I generally get the whole "killing is wrong" bit, but it fits in some cases, and not in others. I don't think it really fit in with this game, especially given the dark "Revenge Solves Everything" tagline. I'm supposed to be some scary steampunk "Count Of Monty Cristo", the story shouldn't have a bad ending if I refuse to basically pretend I'm Batman and refuse to kill anyone. Batman has his own games, and the non-lethal aspects of things work in those games because they were designed for it. Nobody designed 47 awesome ways to kill into "Arkham Ciy" and then punished you for using them, instead they decided "Batman doesn't kill, and we don't want him to in this game" and kept to that theme through the design and what tools and moves they give you, making things substantially more "organic" so to speak, I never felt like I was being forced to hold back the way I do in Dishonored.