Well that svcks. I hate when a game does that. I would rather just kill who I want to and not worry about the consequences.
Do that! Seriously, just do it. If that's the way you want to play, then go for it. You'll probably have more fun with it (I know I do) and it's not going to make you get a "worse" ending, just a different one.
While I can understand what Arkane was going for with this mechanic, I think it's one that's often unclear to players, who can feel constrained or conflicted about effectively playing the role of an assassin while thinking they're not supposed to kill people. We're conditioned in some ways to think that doing so will lead to a "worse" ending. While I like that they've implemented mechanics by which there's some consequences for your choices, I think they could be explained better so we have a clearer idea of what to expect.