Couldn't you set up 2 gamepads, and replace the keyboard controls with the gamepad controls using Xpadder or something? That way, each player could take control and you could manually designate who is who in battle.
That, and you could always have one person use the keyboard and the other a gamepad. Sure, the other player can screw with you, but if he/she is reliable, you guys could switch whoever controls it and take turns running around when the other is tired.