The tone of the movie's ending suggests to me that we are supposed to believe that disaster was averted without Charles actually killing anyone.

I'd never considered anything else, I guess, because it simply would have seemed unconscionable for Charles to go on the way he did at the end of the movie if he actually had killed even one person.

I think I've also been short-sighted about the events at Alkali Lake, because I'd considered the big moral conundrum to be how in the world Charles could ever forgive Erik for putting him in a position to kill the entire human race. (Not that he's never done that before, of course, but, still...) I hadn't really given much thought to what actually happened - only what might have happened.