This is a cross post from my blog here.
Most games can't really question the morality of killing. Mario never questions if killing Goomba is okay and Resident Evil doesn't question the morality of killing zombies. Bioshock brings up moral questions, but those are limited to the little sisters and not the hoards of people you mow down to protect them. You could say this is part of a culture that glorifies killing and while that may be true a simpler answer is they can't question it without seeming hypocritical. I mean, how can they really ask you to question it when they mandate you to kill to progress? If you can't progress without killing them making you feel bad for doing so is anti-fun. That said, Spec Ops: The Line is a game that does exactly that and is brilliant for it but I would maintain that game is soul crushing and its atmosphere isn't exactly conducive to a Mario game. This is exactly what is so interesting about stealth games though, because stealth games are one of the few genres that can repeatedly force a player to confront the morality of murder.
In stealth games, killing is optional. Depending on how it is balanced killing can be either a terrible idea or the most convenient path but a big piece of them is that you can avoid enemies. In most games killing is a thing you do to progress and the only times you question if you want to kill something or not is if you have to go out of your way to do so. This is often why scenes where a video game character chooses to spare someone seem so silly, the main character is hesitating to kill the big bad leading everyone but doesn't question mowing down everyone to get there. In Dishonored, you don't have to kill people. You can avoid them but each person you avoid is another potential problem you haven't addressed yet. So what is your tipping point, how hard must something be before you take the easy way out and kill? How much annoyance is your morality worth to you?
This is a prime example of moral choices through gameplay and not though choices in the story. There is no prompt asking if you want to kill or not but a continuous stream of choices and balances that must be struck. This is easily my favorite thing about stealth games as most games don't' have such a natural moral choice ingrained in them.