...This was unnecessary butchery, on reflection. It'd have been very little effort to stun them and maroon them somewhere.
The SI is still in wipeout mode, not post-victory mode. Citadelians who don't make it past this test get removed from the universe. I'd hazard that if he runs into a surviving Citadelian ship later on, and they're still in a bandit/conquer/fighting mindset, he'd kill all of them too.
Essentially, this is not so much a war to be won, leaving the loser to lick their wounds, as an ongoing eradication of the Citadelian mindset from the universe. Those few Citadelians who can rise above it will probably be left alone, or at least not actively hunted down. Any others? Assess and potentially kill on sight.
Citadelians are a clone race, so with their own cloning facilities destroyed they would need to find another civilization capable of cloning their biology if they want to repopulate. This will either mean stealing/conquering such facilities, with the Orange Corps likely to turn up at any point and sterilize everything within half a parsec, or being able to socialize effectively enough to be able to beg. borrow, rent, or buy such facilities - at which point the SI will most likely turn up and assess the socialized Citidelian mindset for likelihood of being able to integrate with the local interstellar community without falling back to their previous M.O.
Is an ongoing counter-campaign of extermination/genocide a little over the top when compared to most examples of conquered countries/people throwing off the yoke in our own history? Quite possibly. But I'm willing to bet that the lack of gentler approaches being taken here is somewhat due to Orange influence, which tends to connect desires very directly to results without much in the way of social niceties, particularly when there aren't other people around to act as sources of appropriate morality. I should also note, in that context, that Paul's actions tended to be more nuanced and moral when he was surrounded by teammates and people whose opinions he valued. At the moment, we have a Paragon who is cut off from almost all of that, and a Renegade who has surrounded himself with friends, allies, and alternate points of view. Result? A colder, harsher, more brutal Paragon, and a softer, gentler, fluffier Renegade. It's not just "the story isn't what it used to be and now it sucks" - what's happening in both timelines is a logical and direct result of orange light use and choices made. (Relevantly: the Renegade hasn't gone to Vega alone yet and also had a long stretch without wearing the orange ring. Not sure if New God physiology is also providing a certain degree of resistance.)
With all that in mind, I can see why Abra Kadabra was so terrified of Orangest Night.
