Seeker,
People, Cyke bites the bullet. He´s disintegrated by Jean. Maybe he´ll be re-integrated by the end of the film to kick Juggs´ unstoppable ass, but for a long part of the film he will be as dead as Marsden´s acting skills.
Sadly, I think you're right. I can just see it: Cyclops is grieving Jean by the lake, blasting his optic beam into the air in angony. She then appears from the lake and he is dumbfounded. She tells him to remove his glasses - believing she is powerful enough to stop the blast. She stops it and they smile and embrace but holding onto the beam causes him to turn to dust while she holds him.
Shortly after, Wolverine (looking for Cyclops) arrives and Jean levitates the glasses to Logan and explains what happened. Logan is both amazed and frightened at what occurs. She faints, and he takes her home. She then escapes and Prof X and Magneto go to her house to stop her - they know how powerful she has become. Only Magneto survives her attack because he is wearing his helmet. Prof X dies. There is a combined funeral for Scott and Charles, leaving Wolverine and Storm to lead in Jean's absence. Wolvering - once the outcast and rebel - now must take charge in the final battle against Magneto.
If anyone can come up with anything more plausible, I would really like to hear it but I think this is what will happen.