That wasn't a sanctioned operation, though, those were Hardin's loyalists. It also wasn't a random culling, it was--as you noted--a response to what they took as a betrayal. The real question is how much McNamara and Veronica can influence the Brotherhood onto a less fuck-the-world path. McNamara would likely at least take up the offer of "I will give you back Helios, on the conditions of 1: make sure that ARCHIMEDES remains offline and 2: let these guys in the lab coats pick over the building for any non-military tech that could improve peoples' lives." McNamara is about the best shot that the Brotherhood is ever going to get to lighten up, and it would be a shame to not at least give them the chance. If everything goes to shit, then as
@Snekposter mentioned, there's always the securitrons.