That wasn't Jean, though. It was Phoenix-as-Jean. The real Jean was recovering from injuries in a cocoon at the bottom of Jamaica Bay. Reconned before being published or not, that's the story. X-men history.
This latest "Scott's a dick" thing isn't the only reason Cyclops is disliked by a lot of X-men fans. He's been a dick for quite some time. I actually feel for the character. How is going to feel when, after the Phoenix Force leaves him, he recalls what he did? Remember, Scott insisted the PF be allowed to come to earth unopposed by the X-men, despite Tony Stark's stupid weapon that split the entity (I still find this event very bothersome).
Not that anything could have stopped the Phoenix, anyway.
While it is very true that it was the Pheonix "entity" that wiped out a whole civilization, that was not the case when the story was written. Claremont and Byrne said so in later interviews. Even Xavier....EVEN XAVIER was prepared to fight for her life even when he knew what she did. For those who don't remember, go back and read it again. The whole "trapped in a caccoon" was a retcon added on after the fact. It still doesn't change the fact that poor Jean was seen as a victim during that whole story. Yet, Cyclops is seen as a "prick" because he is doing the things that must be done. Even Wolverine, who is KILLING PEOPLE is seen as more of a hero than Cyclops. Heck, the whole X-Force team is seen as heroes. Yet, Cyclops is a prick because he won't take shit from anyone when it comes to mutants who were down to the last 198 or so.