I also see us allying with one side or the other in the game.
I foresee the game will present us with the "Heroes on Both Sides" equation as we see Reasonable, Evil, and Unreasonable members of both parties. The Venatori will be there as a representative of "evil" mages while the Red Templars will be the same for the Evil Templars. I don't think either side will be annihilated but I think the Inquisition will be permanently replacing the Templars in the setting's lore.
* I think that Vivienne will be very Pro-Chantry but having a disdainful opinion of the Mage Rebellion overall.
* I think Varric is going to have a disdainful opinion of both Templars and Mages as he, like so many, are well and truly sick of it now.
* Cassandra will be moderately Pro-Templar.
* Dorian will be Pro-Mage even if he's somewhat removed from the conflict.
* Solas won't care one way or the other.
* I have the idea Blackwall will be sympathetic to the revolting Mages.
* Sera will think both sides suck.
* Iron Bull will probably express some amused concepts at Free Mages in general but in a good-natured way.
* Cullen will be very pro-peace between both factions and surprise everyone expecting him to be Pro-Templar.
Basically, I don't see anyone really having a big stake in this.