I would do the same as if a small character used a heavy weapon, or a medium character used a large weapon (as from an ogre or such). He attacks with disadvantage.
I don't think more than that is needed for game balance. Disadvantage is a pretty strong penalty, equivalent to about -5 to hit, while using a 2-handed weapon in one hand is really not a very big bonus, equivalent to about +2 damage and perhaps reach.