In fact Emma, Namor, Magik and Colossus all did morally bad things (Namor drowning Wakanda, Emma brainwashing) while Cyclops was doing good stuff like fixing natural disasters and stopping them from being more evil. All of this while they were under fraction of Phoenix Influence

Cyclops only killed Prof. X and put the earth in danger after he was under the influence of the full Phoenix. Which is understandable given Jean Grey committed genocide while being possessed by the full Phoenix.

It’s actually funny because if we contrast him with the other Phoenix 5, he comes out as the one with the strongest moral fortitude. While it would’ve been completely understandable for him to become more villainous. Yet the writers didn’t do that for some reason.