You will choose one side to help you with the Inquisition, and not choosing the other will have consequences, such as maybe that faction turning into one of your main opposing groups. But it's one noisy faction after your neck, not every single mage or Templar in the world. Most of those who don't want anything to do with this conflict are hiding with the Grey Wardens these days and not fighting in the war for either side.
I really doubt it will come to such extreme scenarios, though, because as I also mentioned earlier, Gaider has said before that they learned their lesson from the Dark Ritual/Ultimate Sacrifice situation and decided to never fracture the world into irreconcilable alternate realities again. You can't have either "total mage freedom" or "total mage annihilation" without splitting DA into two completely separate games, and they're not doing that. These will probably never be player options at all. We'll never be able to completely free all mages or completely exterminate all mages - if either one is ever done, it will be by the plot, not by our choice.
The most likely scenario for Inquisiton at this point is that it will be like DA2 - we'll get branching questlines and reactions from the world during the course of the game, but in the end every major decision we've made will be reconciled into one event or scenario that can be carried forward into DA4 with minimal conflicts. In DA2, it ultimately didn't matter who you sided with; in the end Anders still did the thing and Meredith still did the other thing. We'll probably see a repeat of that here: we'll see changes in the game depending on who we side with, but ulimately it won't matter because (Character A) will do the thing anyway and (Character X) will do their own thing, and we'll have an ending that's cohesive for all players, regardless of our personal choices.