He earlier too went really quickly to just "butcher the marauders" and hasn't seemed to consider the idea that normal people in a dangerous and shocking situation can attack reflexively if approached by a dangerous looking group. He doesn't have to say he'll be killing civilians, the possibility is still there. And keep in mind Six doesn't know these people, he hasn't interacted with them before and this first mission has been a really stressful one. He doesn't have a baseline for Rennac yet to look at to say "oh he'd be plenty careful not to just kill innocents".