Not to defend the plot of Children's Crusade, which had gone completely off the rails by that issue - but there was an in-story justification for that. She was going to repower mutants one at a time, and had offered to do it, but the X-Men refused the offer, demanding to take Wanda into custody instead, and it devolved into an Avengers vs. X-Men brawl. She then explained to Patriot that the only way to save mutants is to reverse the spell before the Avengers and X-Men arrive to imprison or kill her, and the Young Avengers then argue over whether she's right: Billy, of course, agrees with her, suck-up that he is, but so do Cassie (poor Cassie) and Teddy. Does any of this really make sense? Of course not, especially the kill-crazy writing of the X-Men. (Scott is offered the chance to reverse M-Day and says no? What?) But the explanation is in there.
The "makes decisions for all mutants unilaterally" thing does seem to have become a pattern with the way writers write her, probably because they're all trying to put spins or new twists on M-Day. It would be nice if the Uncanny Avengers disaster showed her learning a lesson about this, but nobody really seems to have learned anything at all except that they should be nicer to each other.