How do we know Scott is "dead?" His glasses were floating. No body, no limbs, no blood. Nothing to show he was gone. Jean just depowered him and wiped his memories. So, he ran off, leaving his glasses behind. Xavier somehow knew this (maybe he read Jean's mind), so he didn't acknowledge the "death." Because she went ax-crazy and they had to deal with Magneto, he never got around to saying, "Hey, the Team Leader is not dead, but he has amnesia." So no one knew, and everyone thinks Cyke is dead.