Professor X was pretty much doing the exact same thing as Magneto. When it came down to it, they were both unethical preparing for a war.
Professor X and Magneto actually both cede to this point in X-men Legacy after messiah complect. When omega sentinel asked them both which side was right, they looked at each other and agreed they were both wrong.
Later both cede that Scott Summers had a better vision of mutant kind than either of them, being the middle of them both