My understanding is that XMFC is intended to be a prequel to X-Men and X-2 (What X-3?), and presuming that is correct, yes: Charles' paralysis is canon.
Also, from things James McAvoy has said, he believes it to be canon. Whether that has any meaning, I don't know, but.
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Also, from things James McAvoy has said, he believes it to be canon. Whether that has any meaning, I don't know, but.