Can Apocalypse even manipulate human matter? He was able to manipulate darn near anything, but when it came to dealing with humans, instead of turning them to dust he instead decided to put them through a wall.
If he can't manipulate biological matter, Superman stomps.
He did it with Angel. He made bones pop out his back and then transmuted them along with the rest of his wings into metal. It was a pretty gruesome and cool scene. He never turned people into dust, but I assume he could affect the biology of others since he could amplify the powers of other mutants, and physical changes occurred, like Storm's hair turning white and Angel with metal wings..
He was also able to physically hurl people with his telekinesis, so I think he can affect humans directly too.