So what really happens when a rather hated character becomes heroic all of a sudden, in comincs ? He dies. And Jean is a pro at dying and resurrecting, so it won't be shocking at all.
What is gonna happen is, young Scott is gonna Martyr himself for Xavier's dream, and in doing so is gonna give current Scott the change-of-heart needed to get back to his old-school ways. The timeline will not change, the rest of the O5 will go back to an alternate timeline without Scott. Bendis himself said that there is gonna be a big price to pay for all the time-hijinks.
After all, Marvel now needs a death to rival Damian Wayne, and who better and more shocking to kill off than a young, heroic Scott Summers, eh ? Controversy = sales.