yeah but there is a difference between movies and comic books, mostly fans read comic books, casual audiences see these films which is partly or mostly where the money comes from
if you look at how the movies have been so far its been Xmen vs the brotherhood for X1, xmen with help from magneto to save Xavier for X2, Xmen vs Magneto X3, origins with Xavier cameo, first class the beginnings of Xavier and magneto, with only the wolverine not having any of them
yeah they could get rid of Xavier, but would singer or Fox risk that when they can just keep them in the films and work around them?