What if 'aiming for Mage emancipation' entailed acts of horror that would not be condoned by either side? Summoning demons? Mind controlling civilians into supporting the cause? Murdering fellow Mages to stil up additional resentment and/or prolong the conflict?
I think we the PC will be able to summon demons (you might not even have to be a mage) and mind control seems highly possible as an option for blood mage PCs, so neither one would necessarily make much sense as something to force opposition to. The latter I would chalk up to "betraying the principles of the rebellion," so yes (not that the first two aren't, but I don't think the Inquisitor will be forced to be better anyway).
Not ending the war =/= choices don't matter. I'm not saying that siding with mages or templars shouldn't have effects in the game or lead to the same content like DA2 did. That doesn't mean that the war has to end to have effects.
But I honestly think it's time for the war to end, and for us to wrap up most of the issues in Andrastian Thedas; they've been going on for years IRL, and Dragon Age has a lot of potential to look at other things.
Depends on what are the outcomes. Having the Circle as one outcome and no Circle in another is fairly different and difficult to merge in a similar situation.
I am almost positive that the Chantry-controlled Circles will not make a comeback. I think the choice will be how the Inquisition chooses to conduct the new system, as I suspect it will, but given how often protagonists vanish, the Inquisitor may well not be in control of it for long.