Honestly If Aymeric and house Fortemps aren't our allies in Ishgard, I'm not sure who would be. Ishgard is clearly going to be an ally for us. If we were enemies of the state openly I don't see us living in the city which we will be doing since it has the zones marketboard and will house various important NPCs like Rowana. I seriously doubt this will be a Dragons=good, Ishgard=bad story. I suspect we will in the end see both sides are being played. Nidhogg is strongly being presented as an enemy.

Also being Faithful doesn't mean being blind. They are faithful to Halone, not the Holy See. Its the principles of Halone which would guide their actions which actually comes up in the Main Scenario when Aymeric is asked why he doesn't pursue the heretics directly.

I'm also pretty convinced that Iceheart has been played. I doubt she knows a great deal more than we do about the Ascians. We are after all the chosen champion. I think her calling is more related to closing the breach between dragon and man. In fact I suspect her understanding of this comes from the echo. It would have enabled her to witness truths about the past. That doesn't mean she has the full picture and the fact she chose to summon a primal, something that is exactly the wrong choice to achieve her stated goals, means that she has been manipulated. She has never shown any indication that she felt she was wrong summoning a Primal. Quite the contrary. She was angry at us for getting in her way.