Then Mutants would have gone extinct.
Scott was faced with the toughest choices I've ever seen a leader have to make. To make a long set of complicated circumstances into a short summary it was either "Stick to my morals and we all die" or "I cross the line, destroy my name, but in return, this and future generations will go on"
Cyclops chose the latter. There was an entire issue dedicated to Scott making this decision.
Post M-Day Cyclops really stepped up his game.