Yeah, meanwhile you have Leliana, Solas, Josephine, Cole, Blackwall and Dorian who all sympathize with the rebel mages to varous degrees. Morrigan is also a non-circle mage with a head on her shoulders and crucial to the plot. Dorian considers the Circles a prison and highly dissaproves if you conscript the Mages, so yes he has a stance on the issue.
So I'm really not sure where you get the idea Bioware wanted us to think all non-circle mages were idiots. They put dissenting voices in Redcliffe itself for a reason. They just showed mages make bad decisions like everyone else; hell if you don't save them the Templar order pretty much all become Red Templar monsters, they don't look much better. Cory is the Big Bad here, but guess what, the Big Back back in DA2 was a Templar.
They muddled up the issue by making sure it's not Nazi Templars vs freedom-loving Mages like it somewhat was in DA2. Doesn't mean every Mage that doesn't like the Circles is put in a bad light, far from it.
You're not sure where I got the idea that Bioware strongly dislikes Libertarians and like minded people? Never mind that Corypheus is a Tevinter Mage. Fiona, the head of the Mage Rebellion, is portrayed as a complete fool who allied with Tevinter even though she had Alistair at her back. The Mages at Redcliffe went along with Fiona and all three of the people who disagreed with her did nothing.
The Templar Order becomes red monsters at the behest of a Mage who wanted Ancient Tevinter back in all its glory. DA II's Meredith fell victim to Red Lyrium; her behavior can be excused, especially when you find the legion of blood mages in the city and an uncooperative First Enchanter who hides a Serial Killer Blood Magicking Necromancer, amongst the other skeletons in his walk-in closet. Oh and that one guy who started the war in the first place....You can argue all day who's the big bad in DA II, DAI leaves no such room.
Not every mage who opposes the circle is put in a bad light, true, just the more important ones. Like Solas who