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I didn't play 1.0, so I don't know anything about FFXIV's history. All I know by the opening scene is that Bahamut is an Elder Primal that brought Eorzea to its knees. But the question I am asking is one that concerns the spell they used in attempt to seal Bahamut. Was that... Holy? There's been connections between Bahamut and Holy in the previous games, I'm not sure if that is the case here.
It wasn't the Holy spell, but holy in a general sense in that it was actually an attempted summoning of Eorzea's pantheon of gods and goddesses - the "Twelve' (hence why their glyphs materialized during the spell's casting). Louisoix was using the entire planet's aether as a power source to resummon the Twelve back to the corporeal realm in order to reseal Bahamut within a new Dalamud (there was a quest in 1.0 where he sent the player out to the Deity Stones scattered around Eorzea to pray to the Twelve as a prelude to this.).
Unfortunately Bahamut was too powerful and managed to break free before the summoning of the Twelve could be completed, and thus the plan failed.
That's the basic explanation of it anyway. :)
To be as clear as possible, Louisoix chose to not fully summon the Twelve. To do so would have run the risk of draining the lifestream too far and leaving the realm lifeless. He summoned their strength alone, thinking this would be plenty... but, alas...