I disliked the pro-templar quest personally. The dream sequence with Envy was cool, but I very much disliked babysitting Ser Barris. That fool templar should have been able to hold his own. I also don't understand people's obsession with him. He's kind of a coward in my opinion. I mean this supposed KISA watched an old women get punched in the face, and he just buckles under the combined power of authority and peer pressure, remaining silent. Not until everything goes to absolute s**t at Therinfall Redoubt does he think, "Maybe I should stand up against these red templars?"
I think if the Inquisitor goes to meet the mages at Redcliffe and learns of the threat of time magic, then the Inquisitor has more reason to go after the mages than the templars at that point (from a role-playing perspective the player's knowledge is separate from that of the inquisitor's). Time magic is more of a threat than an arrogant Lord Seeker from the the main character's point of view, I'm sure.
But not everyone truly role-plays. Many people self-insert with full knowledge of the game's eventual outcomes. So, in the end... whatever the player thinks is the best quest is the better story.
I think you can RP different characters who would feel different ways. In my first Templar playthrough, I am playing a female rogue/archer Lavellan who is anti-magic in many ways and distrustful of her Keeper and magic in general and who has a few encounters with human society before the conclave, including being saved from a remnant in the woods by a few traveling Templars. She comes to realize, through Mineave, that though she thought her clan had other ways, they were actually sending extra Mages into the woods - not a good system in her eyes, as she looks at the human Circle system and thinks it ideal for containing mages while treating them more humanely than sending them off on their own at 7. Minaeve also shares how Templars gave her food and were helpful. Vivienne shares how they can be helpful. Cullen is nice but mentions abuses that must be stopped. Whenever anyone talks about siding with the mages, all they mention is "freedom." Well, as a Dalish, Lavellan has seen her share of a group grasping at freedom - and she is skeptical that the kind of freedom people fuss about actually exists. Now, she was a bit sickened by the Templars at Val Royeux - they seemed to do their duty poorly. But she has no desire to work with Tevinter, and she is equally sickened by the Mages choices. She met Dorian, but didn't trust him. The clans don't go that far North for a reason. She also worried that mages near the Breach would lead to abominations, something she is terribly afraid of (she's scared of demons and such). I had no trouble with her consulting the Templars even after going to Redcliffe - her plan was to try and convince the Templars to help her take back the Castle. It's not like when RPing, I know I will lose the chance to deal with the other situation entirely - you're just picking who to best help with the Breach, which she felt was the Templars. Her impression of the mages was that even the ones who disagreed with the conscription were going to do what Fiona said, for whatever reason - three complain, none of them give good reasons, and she doesn't understand why they don't just leave the Mage Rebellion and come with the Inquisition if they're so unhappy. A distrust of mages and magic will get you far with RPing, and it's not odd for the universe. And this is a weird example because an Elf admiring the Templars is a bit odd, yes, but it felt natural with the background I had created. Inspired by Mineave.
As for Ser Barris - I think that guy is awesome and he does feel badly about not standing up sooner, but I think people underestimate the power of the chain of command in military forces. It is absolute. That he stood up ever, that he expresses doubts publicly when you arrive and at Val Royeux, these are all brave, considering he's part of a military-like Order. As to running back to the Hall, I think it's dumb enough that your party eventually kills the demon without the Templars there (I headcanon they weakened it) because really it taking 30+ low-level templars, a butt-ton of lyrium, and a few Veterans to hold off a powerful Envy demon for awhile is one of the best representations of how Templars really fight demons and abominations so far, in terms of matching the lore. .