Well, I'm still rereading this. I just finished the Xorn stand-alone issue, and now I'm definitely sure Morrison made up Xorn's identity as Magneto much later on. Of course, there are the various hints and nods such as his talk about creating a new world in the annual, and only healing nano-sentinel infected people in Imperial, but...
In the one-shot, Xavier looks into Xorn's mind. Xorn asks him what he sees, and Xavier talks about how Xorn's brain is a star which holds incredible power, blah blah blah. How did Magneto trick Xavier into thinking that?
Also, Xorn goes after that monster thing. When he finds out the mother is committing suicide along with the child by overdosing on pills, he offers to heal them. If she had said yes, what would he have done then?
Later on, once the monster has been killed, and many people are injured (most of them from an explosion), it shows a panel of Xorn healing a person who has been knocked unconscious. How does he do it? Pretend to heal them?
Gah - so far, I'm pretty sure Morrison made Xorn Magneto when he needed an idea for a story. If I find any more hints that either agree or disagree with this notion, I'll post 'em.