the story line promoted not killing anyone...
Were you playing a different game than me? The story constantly encouraged you to kill, although it did reward non-lethal styles with a calmer, more stable city (which is quite appropriate, in my opinion). After all, you were rescued to become an assassin for the loyalists. I'd say that's pretty encouraging toward the "kill all enemies" approach.
Mind you, I usually prefer playing non-lethal (as with most stealth games, when given the choice), though I did a recent lethal playthrough.