The only thing I really didn't like about this conclusion was the fact that Kitty choses Scott over Ororo, Logan and Rachel. She chooses Cyclops over her two mentors and father-like figures and her best friend, yeah, I get she feels kind of betrayed but come on!
Other than that this was a pretty damn good conclusion for a not that good event.
Scott killing Xavier wasn't what made everyone hate him. They hate him because he gave up on the dream. Logan has killed more and has done worse things, but he has never stop fighting for Xavier's dream. In the end, since the 'no more mutants' thing Scott has walked a darker path. He now belives on Mutant survival, not on the whole human/mutant coexistence dream.