@IoannesBellator, I think your cherry picking details here. We are shown several good clerics in the Ishgardian Church in the MSQ and in side quests, ie. the one who spends most of his time in the Brume. As for Thordan, he dissipated after his defeat. My guess is his ritual screwed him over and consumed his own Aether. Note that the same happens to his Heaven's Ward and we barely touch most of them. They screwed with powers beyond what a human should and it blew up in their faces. And he literally goes on about becoming god king of the world and enforcing order on the world. For the WoL, summoning a primal is never ok. It consumes the life force of the planet. Infact the only 'evil' priests we are really shown are the archbishop and his personal guard and even they are given a justification, however misguided, for their actions. The love greys in this story.

The greatest irony is that you call Gridanians tree huggers where the spirits they worship are both real and far more dangerous to ignore. The elementals triggered the 6th calamity due to the hubris of men and their abuse of magic. Those are spirits you want to take very seriously. In FF14, you screw with nature and it can pay you back in spades.

Ishgard was a far from righteous society but it was mostly due to class imbalance rather than religion. The flaw in this lay in the individuals in power not the establishment.

I'd like to add that all the city states have notable flaws. Gridania struggles with xenophobia within its culture, Ul'dah has extreme corruption and Limsa is literally run by pirate factions. I think they did a good job of portraying both the good and bad traits of Ishgard as well. The issue with the origins of the war were born around the social imbalances which were hidden behind the lies. The reality is that the Noble houses claimed their higher status on a false premise. The fact that successive Archbishops supressed this, allowing for social injustice to become problem. The reason Aymeric went to speak to the Archbishop was to try and convince him to proactively reveal this truth as if left to spread on its own would trigger social unrest among the lower classes. While the argument that it would be a terrible cost to the public to know their fight was based of a lie, the lie itself allowed for the social issues Ishgard had to develop.