How exactly does allying with the templars remove every corrupt element? As shown by what happens if you side with the templars in a Divine Vivienne playthrough, they are outright rebelling against her because she's a mage, pretty much showing that they are still the same mage-hating a-holes they've always been.
Well, it's been argued by several people here on the forums, including myself, that having Vivienne as Divine is a solid first step towards becoming closer to Tevinter by giving a mage so much direct political power in the day to day lives of everyday people. And considering the religious doctrine and teaching, some of which templars have had from childhood being raised as orphans in the Chantry itself, like Alistair was, and it's really not surprising that they would rebel against a mage having direct power over their actions.
As Cassandra said in regards to the Seekers actions as a result of the mages declaring independence, the result was predictable.
What I feel is removing the corrupt elements are this. The people pushing to slaughter or force mages into a situation that is otherwise intolerable have been gutted out as we strike down the leaders with the sword. Then you have Cassandra keeping the more fervent ones in line as a Seeker, especially if she reforms the Seekers with full disclosure of their past actions.
And if we ally with the templars, Ser Barris acts in several war table missions, defending mages from mobs, dealing justly with his charges, and remembering the solemn duty of a templar. Protect the world from dangerous magic, and protect mages from the world. He treats the mages with dignity, respect and as people. Then he can be promoted by the Inquisitor to be the new Knight-Commander.
He is a man who will not be ruled by the mob, knows the full extent of his duty, and deals justly and fairly with all without discrimination.
Between him and Cassandra's reforms, this solves pretty much 90% of my problems with the Circles and rest is just small stuff that likely would and could be handled individually by each Circle.
DA2 pretty much showed the absolute worst of both sides and convinced me that the templars were corrupt at an institutional level as the vast majority of the problems in that game can be linked to or related to templar abuse or seizing unjust authority or outright ignoring the legitimate issues, like Emerick trying to solve the murders (which included a loyal Circle mage) and getting stonewalled by Meredith. Inquisition had me kill all the templars who were so zealous that they disobeyed even their own superiors to go on a mage killing spree, or were so corrupt that they willfully purged their own ranks of templars who asked questions or doubted the righteousness of their cause.
I feel that there are solid arguments no matter where one's stance was in DA2 to side with either group in Inquisition; I feel that siding with the templars in Inquisition guts out the corrupt heart and forces them to start over and return to their roots and principles.
Of course, allying with the templars and then having Vivienne becoming Divine is going to cause conflict because even with strong moral leadership, many templars would still be highly uncomfortable having a mage as the figurative voice of Andraste and head of the faith after centuries of being taught that magic itself is corrupt and being taught about the evils of Tevinter and fearing magic.
But I'll let Vivienne deal with that. She likes the templars, so she can deal with their attitudes towards magic and her if she is Divine. It's part of the job and she wants it, so let her lie in the bed she makes.
That's my view on that.