I'm pretty sure just choking him won't work, as I did just that and the mission didn't count as completed until I stuck a sword in him..
Yeah, although the game doesn't explicitly give you the option in the mission briefing you can do it (although I decided to off him in mine; one death wouldn't hurt my low chaos rating). Solutions:
Went back and redid it. Had to be done.
[Spoiler] Just done the Regent mission. Knew what was coming next. Not because of the story, but cos of the limited missions I had done. Plus picked up the explosive pistol plans, but had completely forgotten about the assassins.
Is there a non-lethal takedown for the torturer?
1. Take out the dog with a sleep dart (not that killing animals affects chaos, just I think the 'death' noise is more likely to alert the torturer).
Then either stop time and sneak up behind him to choke him out, or alternatively blink behind him and do the same thing.
I think once he's finished flailing the corpse then he goes into a patrol type pattern so may be worth waiting around a little and then striking.
2. Just avoid the entire quest altogether, it's only a side mission so you don't have to do it. Though if you want the rune I guess you might as well deal with him while you're down there.