I think it's impossible for any dogmatic religions based on the worship of a god or gods to exist without hypocrisy. The Chant seems extra hypocritical in comparison to the flexibility of the Qun, and the Elves have more of a culture than a religion:at the very least the creators don't seem to have any divine mandate; the same goes for the Dwarves.
The Chantry exists and operates in a world filled with intrigue and political disputes. And it's made up of thousands of different people. You have polar opposites like Elthina, who sees the Chantry as a"gentle Mother" and Lambert/Meredith who believe in harsher approaches; all of them are devout Andrastians. Basically, I just think it's mostly useless to accuse a giant religion of hypocrisy; especially given the context it exists in.
Even in our limited exposure to the other religions of Thedas we see their hycrosies as well--
Dwarves- we are all children of the stone, except for those of us who are casteless or no longer live underground. They aren't children of the stone anymore. Well they are if the make a huge sacrifice or join the grey wardens, but other then that they are nothing. Unless a casteless has a son by the nobility, then they are again children of the stone along with their entire family. But thats it.
Dalish-We don't consort with spirits, except for when we do to benefit our knowledge or further our revenge plots. There is also no
Qun- We don't see how you can attach significance to an unknown god that is you have never seen, but we will basically throw our entire life away if we lose our sword.
NOTE to READERS: This isn't an attack on those religions just a basic idea of quick hypocrisies I could think of to demonstrate the idea of calling a religion hypocritical is ridiculous. No Lob, I don't need a defense of the Dalish. I am not attacking them. No Dragon I don't need a defense of the dwarves I am not attacking them either.