Well Xavier is already crippled.
I'm not going to try to explain my way out of Xavier walking in X-Men: The Last Stand (or in X-Men Origins: Wolverine). It's a continuity error, plain and simple. It's just not one that's gonna have me running around like a chicken with my head cut off screaming "REBOOT REBOOT!" especially considering it's a detail that doesn't really change the narrative.
As far as I'm concerned, the timeline is still in tact, with the rift between Xavier and Magneto not being fully completed, and they are able to come together to help Xavier recruit mutants for his school (and build Cerebro, which is how he finds the mutants).
So Magneto would effectively be crippled already, as established by the events of X-Men: First Class, and the conflict of ideologies, further amplified by the Jean Grey situation, would cause the final split between Magneto and Xavier.
That's how I'm looking at it anyways.