Like the Jedi the mages would have to be above petty concerns like nationhood to make that viable.
That was one of the good points about the (old?) Circles: the Chantry was a supranational institution, so they could rise above national interests to impose an international standard.
Same thing happened with the Super Hero Registration act. The difference is the various nations still want to use the mages when it suits them.And they can't do that unless they have some means of control.
What happened in Marvel's Civil War was a bit different, though. Until that point there were superheroes and supervillains (the moral divide), but superheroes were pretty much liked until a disaster happened. It was difficult to accept hunting people that the day before were just saving you and your family.
We have to understand where mage persecution comes from. Historical perspective is necessary, including in Thedas.
The Chantry didn't decide one day that mages were evil and had to be imprisoned. The root of it it's the old Tevinter Imperium. Their magisters were one of the worst bunch of bastards ever. Not satisfied with crushing down every neighbouring nation except their classist pals, the Dwarven Empire, they enslaved thousands and did horrible experiments. The disastrous Fade Walking that gave birth to the Darkspawn is the most famous one, but DAII revealed others like the Secret of Kirkwall.
So when a barbarian named Andraste comes to the conquered and the enslaved and tells them that God loves them and that the mage overlords can be kicked out, what do you think they are going to do? Revenge! And then Andraste was burned alive by the same corrupt magisters. Only one of them felt guilty, the Archon Hessarian, and then used it to get rid of the opposition to his reforms. Even in Tevinter, muggles killed mages.
Then came the years of chaos. There was no Chantry. There were a lot of cults. Without the Imperium providing support and Maferath's little kingdoms imploding and reforming themselves, a lot of mages were left unchecked. Probably more than one tried to revive the old ways (mages on top, of course). Then came the Inquisition. People forget that part, but at that point in history the crimes caused by mages were more appalling than anything the Chantry has done.
What happened after that is a mystery, that we'll likely find out in DA:I. It wouldn't have been very difficult to sell the "Kill all mages!" stance. But it didn't happen. The Chantry accepted them (with conditions), Emperor Drakon valued their power for the war against the Blight, and the Inquisition merged with the Chantry to do their duty in a more peaceful way. Could it have been done better? Probably yes. Could it have been worse? Definitely. So I hope the game will provide players with meaningful choices akin to those which led to the Nevarran Accords. And yes, that includes being able to support the Chantry... among other options.
(And now I'm sounding like a Chantry supporter; that's my fault for playing devil's advocate)