Well, if I'm being perfectly honest, I'd say I wouldn't have. But if we're going off the assumption some circumstance leads me to dealing with them, I would have gone through a lot of the methods people have already mentioned. Picking apart the most cancerous elements, trying to find those most capable of adapting to a changed Citadel. The chap maintaining Comet seemed sensible, for example. He treated Comet more like a machine part than a person but considering Comet was an enemy combatant at the time of capture I can see the reasoning in that. Not saying it's good reasoning but it's there. So that guy was intelligent, self-reflecting and approachable. If he's like that, there are almost certainly others like that. It would be worth finding them and after the Citadel is broken, I would move to rebuilding it into something better. This story was all about tech uplift on Earth but that isn't the only kind of uplift. It would take time but I'd see it as something worth doing if it keeps the word "genocide" off of my history.