I'm not sure I understand, There... As it appears to me, Thordan never allied with the Ascians, both sides were just playing fools of each other... Thordan thought the Ascians would fall in his trap, and the Ascians thought Thordan would fall in their trap. And Dravania and the Ascians have nothing to do with one another, we only know that Ascians helped summoning Bahamut (And Alexander, probably, although I'm not sure it is said, but I can be wrong).
And yes, I know what Hydaelyn is supposed to be the source of all life... But that's what we're told, and we're not necessarily told the truth... Hydaelyn herself and Minfillia told us so, Midgardsormr seems to be Hydaelyn's vassal, but that doesn't mean Hydaelyn is good while Zodiark is bad. We only know that Primals bleed Hydaelyn dry, enabling Zodiark to return. Thordan wanted to become a new god, maybe, but so he could take care of Zodiark and Hydaelyn, ensuring that no deity would ever intercede in the mortals' life anymore. Honestly... That's not so bad.
And for the twelve's sake, stop assuming things over Thordan, you don't have more proofs that he was going to be a tyrant than I do to prove he was going to be great. He's dead. Maybe he would have been a bad ruler and we would have killed him, maybe he would have been a precious ally, once we discussed with him. Maybe he was enforcing Ishgard's old ways up till the end of the war, because it was needed for him to gather enough power to win it, and would have let Aymeric rule, or any other guy that was good enough for the job. Maybe he was going to rule the theocracy as he always did, being a bad guy. The thing is, we won't ever know.
Finally, Aymeric didn't go to Thordan to reason him, he went to demand that Thordan ceases his actions, and probably take a personnal revenge for being a bastard son. Thordan thought about this plan for decades, and was convinced it was for the greater good, why would he listen to a capricious child that only sees a part of the bigger truth ? Try to walk in his shoes : he had absolutely no reason to listen to Aymeric, nor could he explain Aymeric his plan, since the ascians were probably there.
I still don't get why you all need... baddies. That's a very manichean way to see the lore, I think... Yeah, Thordan was an enemy, but he wasn't a bad guy. Like most FF villains, to be honest.
A gift from Elidibus, probably...