No he wasn't over Jean, and never got over her. Either in Morrison's run or (from what I've read) afterward.
Their marriage was going through a rough patch, they were both changing and handling things poorly. Both of them, especially Scott, were lousy at communicating their issues. Meanwhile, Scott was developing real (albeit confused) feelings for Emma. I think he thought he was going to choose Emma, the reality of how much Jean and his marriage still meant to him didn't really hit him until Jean was killed. I interpret that as the event that finally snapped him out of his funk with his marriage, but it was of course too little, too late. Jean had to telepathically reach back in time with her mind to give him a nudge towards Emma so he could heal, and even then he wasn't over her completely.
Jean wasn't over Scott in the run either. She had a greater destiny as Phoenix, essentially ascending to Godhood, and she had to let Scott (and the rest of her Earthly ties) go so she could save the universe. It's why she seemed colder to him and not able to open up herself. To me, the arc was a well written arc of a marriage dissolving that was sympathetic to both parties and could have healed if not for an outside interference (Sublime) taking the decision away from them. And even then, with comics not having an ending, the possibility of them getting back together is always on the table. They may be stronger because of it.