Well I would use this as a precedent:
A merciful weapon deals an extra 1d6 points of damage, but all damage it deals is nonlethal damage. On command, the weapon suppresses this ability until told to resume it (allowing it to deal lethal damage, but without any bonus damage from this ability).
So its either all or none, bane included. Fortunately, as a melee attack, you can always hit them again (and switch to the other type).