Prepare to be disappointed then. There are societies in Thedas which prove that such a conflict is not inevitable (Rivain, Dalish, Chasind).
Southern Thedas has a thousand years of mage prejudice forcing them into the Circles, preceded by a period of time where mages were simply murdered out of hand, preceded by a time period where mages tormented and murdered their way across the continent and were responsible for the single greatest threat to life on Thedas in existence.
That's a whole lot of hating mages for the populace to get over, and it ignores that mages were just responsible for a demonic invasion.
And, looking to the future, we have another mage who's stated goal is to rip another hole in reality, and probably release some elven mage tyrants to re-enslave their people and wage war on an entire continent of humans. That will certainly endear mages to the common man.
The non-Chantry, non-Qunari Rivaini don't live in harmony with mages, they are ruled by them (and still admit problems with abominations). The Dalish likewise are ruled by Mages, and the focus has been on them being vengeful lunatics or tragically ineffective in their positions. As for the Chasind, we have so little information about them it is impossible to even speculate on how their society works.
One constant keeps coming up, however, and that is that normal people and Mages can not co-exist as equals in any meaningful way. Even the single mage we'd seen living outside the Circle prior to DA:I used fear of his magic and his golem to torment his home village.
No, I don't think the Nug Pope is going to handwave away over a thousand years of fear and hatred, backed up by modern examples, for any meaningful length of time.
Even if you can claim some goodwill from Mages helping out in the Breach crisis, you still have the College of Enchanters led by a woman so monumentally stupid that she started a war with no idea how to prosecute it, lost that war, sold her people into slavery over a bluff, and alienated the formerly mage sympathetic monarchy that had freely offered them sanctuary (by giving Ferelden's most important defensive fortification to a foreign force, led by a mage). With that kind of leadership, mages might as well throw themselves on the pyre and save common folk the trouble.