The Logos attack can only go so far. You will need to take advantage of this by fighting with Black Mages or Archers. Have any Moogle with 10 JP in this battle, because the fight can end easily by having the Moogle summon Famfrit. Additionally, you can enter the battle while the Charm Law is in effect, and thus the crystals will not dare to use Logos. Alternatively you can equip items that nullify charm, although your stats will still go down when Logos is used.