Perhaps the Ascians were willing to roll the dice on him [A] not turning on them and [B] causing enough chaos to bring about Zodiark's return before resistance ended. Or maybe I'm just wrong in assuming that resistance would end. If someone displays an infinite wellspring of power, don't you just lay down your arms for the time being? Imagine the shock and awe of a defeat at the hands of a Triad-empowered Thordan and the Knights of the Round (assuming he also killed the Warrior of Light). I would expect things to just collapse into the Ishgardian Empire sooner rather than later, lol.
Then again, perhaps the eventual Isghardian Empire - Garlean Empire war would guarantee enough chaos to raise Zodiark.