Of course Methos recognizes Andrew Wiggin as Ender--he's certainly got enough experience to recognize children once they've grown up. But whatever the Speaker for the Dead wrote, and whatever orders Congress gives him, he was on Earth throughout the war, and he won't do anything against the man who ended it.

(I guess he's captain of a ship that was at the planet when Ender got in trouble...gah, it's been so long since I've reread that I don't remember exactly how it went)