The beast tribe summonings had many downsides to them...
Namely that the way they're summoned urges their summoners to forcefully spread faith in them, by and large the primals demand complete obedience (again probably due to the rites used), and on top of that, they drain aether. They're not the same as the primals constructed through the creation magicks of the ancients. I don't think the point is that religion is bad, per se. Ability to use magic in the setting is indicated in the game's lore books to correlate with a penchant for faith (thus why Garleans are predisposed to atheism by and large), and by the end of 6.0, your character is receiving prayer to help them persevere.
With that said, I also agree with Theodric; quite often formal religion is replaced by zealotry in ideologies that can be even worse.