Well, I can see it going either way, because while the possibilities are strong that she kills him, her "Kill me before I kill again" line only comes after Wolverine shows her the glasses and asks where Cyclops is. What the wild card is is how aware is Jean Grey of her actions when she turns into Dark Phoenix. If she is only vaguely aware of what was happening, she could have been aware that while she was kissing him her unconscious mind took over and not known the details--thus, seeing the glasses makes her believe that she in fact did kill him even though she's unsure.
And there's no way Professor Xavier can know for sure since he's having a hard enough time finding out where she is from all the psychic interference she's running.
Furthermore, I think it's possible (though highly unlikely) that once Cyclops realized something was wrong with Jean, he may have instinctively opened his eyes, and she being only somewhat awakened and not focusing on keeping his optic beam from going off, it could have blasted her and left her unconscious.
Just a thought. who knows though? What is for certain is they have wiggle room to do whatever they want.