-Jowan THOUGHT they were going to make him tranquil, he didn't have proof. Also he was a blood mage which is dangerous to everyone around him, what did he expect?
Lily saw the Rite of Annulment on Irving's desk, and Irving confesses that he signed the Rite because Greagoir claimed there was evidence - that he never personally saw, by the way.
-Actually look at the Ferelden circle. Do you see any beatings? Murders? Rapes? Templars cracking the whip? Verbal abuse? A restricted and prison-like environment? No, you don't. What you see is basically a boarding school. People learning, gossiping, experimenting, lazing around, it reminds me of Hogwarts rather than some kind of horrible fear and pain factory of horribleness that people make it out to be. The downside is that you're stuck there. (though you have servants and live in luxury unlike the majority of the population mucking out a living in Ferelden) HOWEVER, once you're trained and have proved you're not a danger to yourself or others (because demon possession and blood magic is a huge and actual threat) you can get permission to leave. Wynne frolicked around the countryside with the warden for a full year, Innes the botanist was given free reign to do her studies at her leisure in the middle of the woods and both were unsupervised. Even though collecting and training mages so they don't become abominations or go on blood magic murder sprees is a necessity, the result seems like a pretty awesome life to me where it could be horrible. It could be like the Qun which again I point to the hypocrisy of hating the chantry for their treatment of mages while thinking the Qunari are awesome. There are multitudes of people with this attitude despite the ones who had a problem with being forced to help Talis. (regardless of what the choice was, people don't like being railroaded)
There are people who run away for a chance at freedom - like Aneirin, who was nearly killed and left for dead because the templars claimed this young boy was a maleficar and yet, we see him as a benevolent healer as an adult. Anders talks about the suicides that took place. It was also the setting for a rebellion because people wanted more freedoms from the templars. It's clearly not an idyllic paradise when a moderate tells the protagonist about how harsh life in the Circle can be, and explains to the newly Harrowed mage, "If you want to survive, you must learn the rules and realize that sometimes, sacrifices are necessary".
As for your examples, Asunder points out that Wynne has freedoms no other Circle mage possesses, while Ines was a Senior Enchanter studying a plant that was said to grow in Blighted soil - in the wake of the Fifth Blight.
Furthermore, you're helping me dismiss your earlier claim that it's because of a "hatred of real life religion" because you openly admit people have their own reasons for disliking the Chantry that have to do with aspects of the organization.
-The point of my post was that people hate Elthina supposedly because she is a person of power who stands by and does nothing yet the same people have no problem with the Viscount who is the same, a person of power who stands by and does nothing. At least Elthina tries to make peace, the Viscount just sits on his hands and makes you run errands for him, does nothing about the growing threat of the Qunari, and unlike Elthina, he had real power. The difference is the Viscount is not religiously affiliated. If there are two nearly identical characters and only one is hated and bashed (the religious one) and the other is not at all (the non religious one) then it's pretty easy to make the leap that real world prejudice against religious people is coloring that opinion/attitude.
There are people who voiced that the Viscount was nothing more than a figurehead for the templars, who wielded true power in Kirkwall. The difference is that, by the codex entry's own admission, Elthina did have power over Meredith as her superior: "People frequently turn to her to mediate disputes - particularly those involving the powerful Templar Order, over whom she holds authority as the Chantry's ranking representative."
An overwhelming large percentage of people say they hate the chantry, but hardly anyone speaks up about hating the Qun or the Dwarven system of ancestor worship. The Dwarven society treats people like dogs because some distant ancestor of theirs stole a loaf of bread. There is no freedom in Dwarven society, people are stuck being the same thing their parents were regardless of their own talents or desires. Zerlinda was told by her family to leave her baby in the deep roads to be eaten by darkspawn or starve to death because his father was casteless. His ancestors were dishonorable and so the baby was worse less than nothing. Who in that society would help her? What system is set up to give aid to such people? None. Who actually helps her? The chantry. Brother Burkel and his small chantry take her and her baby in, no strings attached, no kicking the baby out on the street and back to Dust Town when he comes of age like his grandfather would do.
Were you simply not around when MoTA was released? Many people voiced their displeasure at being forced to side with a Qunari agent, and for letting Tallis get away with a list of Qunari agents. Plenty of people have voiced expressed that they strongly oppose the Qun, and that they have no interest in working with the Qunari.
Regarding the caste system, I doubt many agrees with it, particularly in how harsh it is towards the casteless, which is why no one brings it up - if most people don't dispute it, there wouldn't be a debate about it. People even address it as one of the main reasons they support Bhelen's bid for the throne, since he grants greater freedoms for the casteless.
When the Arl's men and the king's soldiers deserted Lothering and left the villagers to be overwhelmed by the darkspawn, who stayed to help? The chantry priests and Templars. The chantry takes in orphans, feeds the poor, runs a community service like the chanter's board, etc...but who cares about that when they do evil things like talk about the maker or train mages so they're not a danger to themselves or others?
I remember Mother Hannah assuring the Amell Warden that a lynch mob wouldn't kill him - that's another aspect of Andrastian culture that you seem to have omitted, and one echoed by Wynne, who talks about how Andrastians kill mages for things they didn't do. That likely has something to do with their view that mages are cursed, as mentioned in both Origins and Dragon Age II by Andrastians. Even Lambert contemplates, "Without the templars, the Chantry was toothless - nothing more than a bunch of old women armed only with words. What would she do? Try to convince the people, after ages of teaching them mages were to be feared and contained, that now everything was different?"
By the way, thank you for this exercise; the simple fact that you're debating the merits of the Chantry with me, in itself, is proof that people don't simply dislike it because it's a religion. 