McCoy may have wanted Harry someplace safe where even Eb himself couldn't find him. Didn't he do the same thing to his own daughter? So it's possible, even likely, that Ebenezer knew that Harry had been disappeared, had thought someone appropriate had been chosen to teach Harry how fulfil his magic potential. He probably didn't know it was Justine DuMorne or if he had known, might not have known that Justin had gone bad.