“They could have easily had a system tell you which enemies you could kill and which you shouldn’t if you don’t want to branch down the more dark path which would allow you to still kill everyone, not kill anybody or simply use everything and not feel punished for it. But they didn’t do that. They just punished…

It’s not designers fault that the game you enjoy is the game of slaughtering innocent. That’s not point of the game and you should be aware enough to realize that. It’s slap to your face saying that you should not do anything just because it’s enjoyable you psycho.