It makes no difference except for a very few NPCs, and generally the game will try to prompt you with someone asking you to subdue them, and in EA there were a couple enemies that had surrender dialogue when they fell below certain HP and non-lethal attacks could also be used to get them to surrender without killing them by accident. I've not tried this in the full release.
I do wish there were a bit more to it. I recognise that it could get complicated very quickly if characters who should be dead in certain plot branches are actually alive, and to add appropriate dialogue, but it does feel like something more could be done.
