problem was just before that Scott was the one pulling away after Jean had searched for him desperately.
I hate it when writers use their own characterization to justify dramatic changes. Of course he can justify it as he did. Because he's the one who created the cosmic destiny out of nowhere.
It makes it read like he shipped Scott/Emma and needed to come up with a way to get rid of Jean rather than he had a great idea for Jean and relaized that left Scott at loose ends.