People, there is a difference between hating doctrine, the religion itself, and hating the religious as people. The former is perfectly fine (in this sense we are talking about mere injunctions, ideas and stories), the later is clearly morally unscrupulous. It seems that people have to some extent conflated criticism of religion, with attacking the religious as people—such conflation is itself intellectually unprincipled, as it is a form of straw man. I would urge people to contemplate the quote from my above post,
This I tend to hate. I have no issue with as you said of critizing doctines and ideas, but I hate it when people generalize and go "religion is evil" or "all religious people are stupid and evil" This is where I draw the line. Critizie the religion, but the concept of religion is neutral; like any force it can guide people to the hieghts of charity and goodwill but it could also make another person commite the most horrorfic actions.
Also I tend to be a strong supporter of religious pluralism. my own faith(hellenismos/greek polytheism) encourages religious pluralism.
relatedly, I tend to dislike idea that religion=stupid and backwards superstitions. I recall that you mentioned the Caliphate in an earlier post. The thing about the Islamic Caliphate was that it was a golden age of learning. It ushered in one of the coolest eras, where the islamic faith pushed science and learning further. as two examples our numbering system came out of this era as well as the whole concept of algebra. Not to mention the vast learning of the body, and astronomy. They did calculations to figure out the circumference of the earth during this era and were mostly right; they needed to in order to help build mosques that faced towards mecca, because well the earth is round.
Now in terms of the game, I would (or my Inquisitor would) hold the chantry to this exact same scrutiny. If there is a mechanic in DA:I (I doubt this) that would let me reform the chantry (and make it suffer a court for its crimes), and separate the Inquisitor’s state from it, I would. My prerogative would be to create a secular republic, one based on reason and liberty, not fear and faith.
I doubt that. As a medeival setting, keep in mind that even the Merchant republics of Italy were still christians and followed the catholic church, though they often put money and greed above faith. But one couldn't call those republics secular by any definition.Though the Merchant republics are cool, they are not secular. I doubt IG you would be able to turn the free marches, Fereldan, Orlais, Antivia, Rivian, Nevarra, Tevinter, Anderfals and the Qun all into secular republics. Though if you do want medieval merchant republics, either Antivia or the free marches will be good here.
one of my favorite stories of Venice is how they were sad that they didn't have a great Saint. They had a minor saint, Thedore I believe, but anyways the venetians wanted a more important saint. so they chose saint Mark as legend has it that Mark would rest in Venice. Problem was that he was buried in Alexandria Egypt. So the venetians just were like "uh lets just steal it" and they totally did. they stole the corpse of saint mark and brought it back to Venice. IIRC they even painted or put some sculpture of them "returning" the body to venice on saint mark's basiclica 
As for opposing the chantry, I do want options for both supporting it and gaining their favor or turning against it. My first character, Navilia is strongly pro-chantry, but I doubt my other characters will be so much supportive of the chantry. As a roleplayer I want options.