Yeah, I think they very specifically say "non-lethal", they are not trying to imply that you've done "good" by not sticking a knife in your target. I went non-lethal for Lady Boyle, and when that guy uttered his parting line, about her learning to love him, I was kind of horrified.
Very Stockholm Syndrome-ish, yes.
And agreed. Just because the choice is non-lethal, doesn't necessarily mean that it's a kinder, or gentler choice. The Pendleton twins, for another example.... laboring in the mines with their tongues cut out until they died.