In all three of my playthroughs, where I pretty much made the same choices in terms of story, just experimented with gameplay, I always killed them both, preferably with a one-shot-kill method. Not because it would have spared them pain, but because I was under the impression that, at that point, Booker was royally pissed and his first priority was to save Elizabeth.
There was no way either tech was going to walk out of there alive, but Booker had better things to do, and bigger fish to blast away. Whether or not they were just 'doing their job', they were scientists, torturing and indoctrinating a largely defenseless girl for no other reason than because she wanted to be free, and wanted nothing to do with Comstock's plans. So they were dispatched with great prejudice.
Besides, at no point during the game does Booker bother pretending to be even remotely nice or decent as a person.