Anyways... I still treat the Reapers as "people" in one way or another. I respect their sense of "personhood". But that also means I want to kill them. I don't care to see them as ignorant machines that need to be rewritten or who need to understand organics. They just need to die. Just like any other sentient, mass murdering, mad scientist psychopath. No different than killing Petrovsky or Lawson.
If the decision came down solely to what fate the Reapers deserved (and it is not, of course, that is just one factor of many that go into my decision and a relatively unimportant one in the big scheme of things), then I would be lenient. I do not think one can fairly judge the Reapers given the Catalyst. I would not similarly punish someone for their actions while under the effects of indoctrination if somehow I got ahold of someone like Benezia and she was freed from the compulsion.
The Catalyst, on the other hand, would not get off easy, but it does not appear that he "lives" in any given ending anyway save for temporarily in Refuse.
I've heard some folks say "Well they sounded like they enjoyed reaping anyway so they must have been okay with being controlled." This of course I cannot accept because the control they were under may have produced this pleasure in the first place. You are not you while under mind-control so none of that stuff counts IMO. Cripes sake, Phantom!Jack talks trash at Shepard and your squad when you encounter her. Does that mean Jack would normally support Cerberus's cause?
And then there is the argument that there are too many hard feelings against them, so, they should be unilaterally eliminated to make people feel better. I cannot accept that either, because it is basically letting the mob dictate justice. Justice should really only be about two things: deterring further crime from taking place, and removing some menace from society. It should not be about pandering to the outraged masses. I mean, how can anyone dispute the Catalyst saying organics cannot stay civil with synthetics when they are content to commit violence -- against them or amongst ourselves -- over things like hard feelings?
I let Petrovsky live. Only thing really scummy that happened on Omega was the Adjutant thing, but there was some reasonable doubt about whether or not he was truly behind that. In the comic, Cerberus had them before the invasion, so the ones he was using might have already been made or been the work of others he did not oversee. And even if he was responsible, I mean, this is frickin Omega we're talking about. Scum is par-for-the-course there. 9 out of 10 of those victims in that whole ordeal were probably some manner of criminal anyway -- LOL! In all seriousness, they likely were Omega thugs that fought Cerberus as they would any other rival gang, likely not any group of people worth shedding too many tears over.
I had no say in Mr. Lawson either way because Miranda kills him (you can potentially choose his fate if she is not in the scene). If I did, I would consider letting him into the efforts, but likely not. It would be a Knight-Captain Denam situation for me (I conscripted most prisoners into Inquisition service, but had a bad feeling about that one so I opted to put him away).