Scott killed Prof. X when he was possessed by the Pheonix Force, but prior to that, he had already set up a X-Force to be the wetworks branch of the X-men. This decision ultimately caused the events of Schism in which Wolverine broke from Cyclops' team over their differing opinions over whether they should train the new mutants as soldiers or teach them as children. Surprisingly, their expected roles were flip flopped with Wolverine not wanting to harden the children into cold killers like him and Cyclops wants to train them as soldiers for the war against humanity. Basically, the whole "No More Mutants" situation pushed Cyclops over the edge and he viewed humanity as out to commit genocide, so he believed mutant kind should reply in kind. So, in essence, Cyclops is just like Magneto in his goals. Hell, he's actually working with Magneto and Emma who have pretty much reverted to their villainous roles, albeit a bit more complex than before.