He's easily the most powerful psychic on Earth. He manipulates events left and right, puts on a saintly image for himself. He' been doing it for years.
Prof could take down Mewtwo before the pokemon even knew what the hell was going on.
Assuming Xavier is 100% completely and totally willing to kill Mewtwo, he would turn that thing's brain into a blob of goo. There are very few people would Xavier couldn't kill if we truely wanted to.