I also am seriously skeptical that the knockout functionality will allow for the kind of bifurcation you're hoping for, but as a way of putting a hostile Minthara at Moonrise Towers that you could potentially suborn into your quest, I'm open to, I just don't think that without the "heart to heart" that you have with her during the camp celebration, there is going to be that option.
You should check out a game called Expeditions: Viking
Aside from the fact that it's just a really good game, it also has a knockout mechanic that is pretty meaningful.
There are plenty of situations in that game where you are in combat with a villain and your decision about whether or not kill them has a significant impact on events that follow. (In one instance, the villain escapes and gets in my way again in the future.)
It also has an interesting choices, as you have some wars in which there's no bad guy, just a "less good/more evil" guy, but you're gathering allies so you need to pick a side.
The "evil path" is also legitimised because it's about honouring your fighing culture, wrecking stuff and taking what you need by force.
I generally played EV as a "good Viking", but there were times when I came across a wealthy church, and I was like, "You know what? They're jerks and they don't need so much gold," and (nonlethally) raided the church, taking all their riches. The game didn't have a karma meter, so that didn't make me "evil", but it did mean the church hated me. lol