I really don't see the issue here. No matter how deep and committed a relationship may have been initially, people do fall out of love too, and that's what's happened here. Scott clearly couldn't deal with the fallout from The Twelve and grew emotionally distant. Jean had gone through the same before and managed okay, ("The bad feelings go away.") and since she was becoming Phoenix once again, she simply couldn't be as empathic as necessary.
So, Scott came to Emma for help, who initially simply tried to rid him of all of his emotional baggage (and Scott does have a lot of that), not to seduce him. While in this deep emotional connection, they recognized something within each other that made them fall in love with each other. That happens too.
Break ups can be painful and horrific, but sometimes, they simply have to be, especially if you've become so emotionally codependent. Lieber ein Ende mit Schrecken, als Schrecken ohne Ende. as the saying goes, which is to say that a "horrific ending is better than horror without end."