I think that Xavier should be crushed by falling debris. The problem with having Magneto maliciously break Charles is that it would be hard for me to buy their relationship, which is really quite civil, in the later movies. If someone causes your paralysis, I find it hard to believe that you would be able to be that nice to that person.
Now, what I could see happening is during a skirmish with the villian, Charles looks on as Magneto goes totally over the line using excessive force to stop the threat. Charles tries to restrain him but is inadvertently crushed by falling debris from Magneto's rampage. It would still be Magneto's fault, but it wouldn't be purposeful and Charles would realize that there is a rage in his friend that he can't control.