Longshot's elitist view on mutants would make even Magneto blush. Honestly he's a lot worse than Mojo, Major Domo, Spiral and Arcade, the villains of the arc. The three mentioned were just simply performing a legitimate albeit perverted method of execution, while Spiral was only a little misguided. The only reason why Longshot isn't treated as a villain is simply because he was fighting with the X-Men, not against.
If you guys do not consider Longshot a villain, I guess the same would go to the rest of Brotherhood including Mags. A villain doesn't have to be completely evil anyway, none of the sane Ultimate villains actually are.