Plus the whole "outlawing dalish religion so they're forced to constantly be on the move to avoid getting attacked". If you're a good religion, you shouldn't have to make other religions illegal to keep people from converting away from yours.
The Dalish aren't at risk of being attacked when in proximity of human settlements because of their religion. The Dalish are at risk of being attacked when in proximity of human settlements because Dalish and Humans have racial relations that range from poor to outright murderous. The Chantry's only involvement with the Dalish in the current age is via the Templars, and that is from the secular perspective of the fear of free mages (which rule the Dalish).
But honestly I don't mind the chantry so long as they stick to dealing with religious matters. I don't want them making laws or running being allowed to take kids away from their families in whatever country they want, even if those families don't follow their religion.
They don't. Besides that the Chantry and Templars are limited to the Andrastian countries, the Chantry doesn't make laws or edicts either. It isn't a legislative body, nor does it dictate legislation outside of very narrow spheres (which are the Chantry religious body and the Circle system). The Chantry's influence is by the agreement and consent of the countries themselves.
As for sticking with religious matters, there is the unfortunate reality of the lack of alternatives. There are no secular, or even rival religious, bodies that have the popular legitimacy or the ability to bring about, maintain, or keep an international system going against internal and external challenges as long as the Chantry has.
Besides the lack of a value of the separation of church and state in Thedas (where the governments least dominated by the spiritual/religious elite are ironically the Andrastian kingdoms), there's a general lack of meaningful institutions.