There's a possibility that the game's handling of non-lethal attacks will be more sophisticated in the full release, but I don't think we have any confirmation on that one way or another. This is a topic we've discussed a few times here before, so I'd expect Larian have seen feedback, but whether they've wanted to or had time to do anything about it is anyone's guess.
There is, btw, at least one NPC who has some "surrender" dialogue that will be triggered if you use non-lethal attacks and knock him out (or just reduce his HP to a low enough level, so non-lethal attacks aren't necessary but make it easier not to kill him by accident). But generally, as mrfuji says, early access treats knock-out like death for plot purposes.
