I ended up letting Chance die because, as was mentioned above, they ALL made use of the brainwashing, even him. My IA is already pretty much a hair away from Kaliyo-grade ruthless, so their fate was sealed as soon as Kothe made me jump and pull my weapon on him.
My IA is all about tieing up loose ends in the most absolute ways possible, so she usually goes for her pistol. I may have missed some opportunities because of that, but nothing's come back to bite me in the *** after 46 levels, so I guess I'll just keep on keeping on.
Again, that cutscene with Kothe ending up on the wrong side of that barrier, with the shot of us just staring at each other, was absolutely ******, and a great example of why this MMO stands out from the pack in my book.