Scott might have been given more benefit of the doubt if he hadn't been an ass before the phoenix and a deluded "rebel" afterword. Remember, he's going around trying to "start a revolution" now, and he hasn't been a very popular guy with most people for awhile. Even forgetting the fact that I don't believe he was controlled by the Phoenix the entire time (I'd say they were all mostly in control until Magik and Colossus fought each other and lost their powers, at which point Emma and Cyclops probably aren't responsible) but I'd say they were all in their right minds when they took over the world and started doing horrible things to the avengers (like locking them in limbo or telepathically torturing them on Utopia). so, cyclops did a lot more evil while mostly in control, while even the no more mutants thing was done while Wanda was basically completely crazy. Thats the way I see it, atleast, and I've only seen Cyclops try to say he wasn't responsible for killing Xavier. He hasn't seemed to try to say he wasn't responsible for taking over the world or doing bad things to the avengers. Those things are what I think seperates him from Wanda.
Plus Cyclops probably isn't doing himself any favors from invoking Xavier's name while doing his Magnetoliteish revolution thing which is a 360 from Xavier's position seeing as he was all for peaceful coexistence. Also potentially screewing up history probably wasn't a good idea either.