The heart of the answer is that the two events aren't related.
Shiva
The Scions were set against Iceheart because all indications were that she planned to summon a primal, and that's one of the "Threat to Eorzea's Salvation" buzzwords that the Scions always deploy to neutralize. She maintained that her goals were righteous, but she had misinterpreted things at every step. She misinterpreted the contextless glimpse at the past she saw in Hraesvelgr's memory as divine providence - the revelation of her purpose in life. She misinterpreted Hydaelyn's silence as confirmation that she was on the right path, all while Lahabrea manipulated the heretics into creating a new primal. She misinterpreted the primal shade she brought into being as Saint Shiva's soul returning from the beyond to join her righteous cause.
After we fought Shiva and went on to meet with Midgardsormr, Iceheart kept on following that path. She brought down the outer wards of Ishgard and led the dragons to their gates, convinced that she would lead a tactical strike on the church and put an end to the deception ... except the dragons lost their focus almost immediately, unleashing their unbridled rage on the innocents in Foundation. Iceheart left this scene hurt and confused, regretting that she had been the cause of this massacre.
That's why we allied with Ysayle; her regret. Nidhogg was rallying the Horde for a final assault on Ishgard, and Alphinaud thought Ysayle would join us if there was even a tiny chance that her dream of peace between man and dragon could come true. She was supposed to be our introduction to Nidhogg, it just didn't work out that way. By the time Hraesvelgr broke through the rest of her delusions, we'd already formed a sense of camaraderie, and in time she came to believe in the Warrior of Light's path.
Ysayle was never under any delusions that primal summoning could be good, she was just sure that she was so righteous that it was the lesser evil. Pretty much everyone thinks that they're the one that will finally use the Wisdom of the Paragons and not get burned. Ironically, summoning Shiva to fight Ravana would have been the lesser evil if she'd actually managed to accomplish anything with it. Ravana would have drained the land and led a crusade to expand the Gnath domain and we needed him out of the way as soon as possible so the dragons would stop brushing us off. Time was a factor.
When she summons Shiva to fight the Empire, it's just a flat-out self-sacrifice play. All of her delusions had come undone and all she had was her dream of ending the Dragonsong War and her faith in the Warrior of Light's path, so she let the Crystal of Light given to her by Hydaelyn dissolve and used its energy to become Shiva one last time - to die enmeshed with the false goddess that had given her strength and comfort so that we might succeed (and good thing we did).
King Thordan
Thordan was convinced his path was righteous, but his betrayal of the Ascians came after their plans for him had already come to fruition. Even if he'd successfully used his primal form to wage a holy war against the dragons and the Empire and all the "enemies of peace" in the world, Elidibus would have just given some other faction (probably Garlemald) sufficient power to resist him long enough to ensure the titanic weapons deployed would cause a Calamity. He managed to circumvent the aetherial draw from the land (at first) by using the eyes of Nidhogg, and tried to circumvent it permanently in a failed bit to consume the Warring Triad, but it was a doomed plan from the start. Iceheart or no Iceheart, he had to go.


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