I suppose they could be setting it up a Tevinter's magisterium fueled by blood sacrifices from slaves vs Qunari where everyone's brain-washed and all the mages are bound and have their mouths sewn shut...
But, as others have said, that's going to be a really hard sell.
If that's what it takes to actually challenge the moral compass of players again, I can't say I'd mind it. Between those two, I'd be quite capable of choosing either way on subsequent plays. I won't lie that I sympathize with the Qun a whole lot more than with the White Chantry we've been shown thus far in the setting. Despite little exposure to them as of yet, the Imperium too holds more fascination to me than their southern neighbours.
And no, I would not find it in any way comparable to "sympathizing" with ME's Reapers, as suggested by another user, far from it. They are not immortal machines with some obscure imperative driving their cyclical campaign of genocide, what we are talking about here are two competing nations in a lower-tech world with very different laws, of the natural, cultural and legal kind governing it; the outcome of such a conflict definitely would not manipulate the very essence of that selfsame world, which the ME-trilogy could boil down to.
It would certainly help if BW could take a step back and drive home the point that our quaint 21st ct. values need not apply in a fictional society where it is still taken for granted that the rule of the day is, for the most part humanity first, and nobility in charge.
Case in point in DA:I: did noone take note of what can be gathered of the Freemen of the Dales's initial agenda in their defection? Ridding Orlais of the nobility's rule which they - rightly - blame for the destructive civil war it's stuck in, so the people can rule instead. Ignoring them being reduced to dupes of Corypheus - why though; would have been neat bringing them over to the Inquisition as another tool against the civil war factions -, I am actually fairly surprised noone appears to bring this up.
Torture as a welcome part of their society.
"No."
(EDIT: I say this about any society. Once it welcomes torture as an institution for any reason, I condemn it. And some Western nations are right on the edge of doing so, but won't.)
Thing is, despite BW going out of their way keeping torture off screen - rather ironic, given the game's title and that of the organization players build up and all its associations -, it's still done in the Inquisition's ranks as well within the game. It's also made apparent that torture is a valid tool in the DA-setting, like it or not. That BW aren't willing to directly show the 'good guys' doing it and only use it for cheap effect of driving home how much worse the 'bad guys' are I'd see as an unfortunate omission in that regard.
It would further help to keep in mind that Thedas is not our world; it's a fictional setting. Plus, I don't think talking about that specific issue will lead anywhere here.
(Although it sure is amusing how Mr Noble Peace Price Winner(sic!) essentially wants to pursue no legal action whatever as a consequence of that certain affair, but anyway.)