Unhardened Leliana's approach is very idealistic, but you do not bring about sweeping radical changes without causing dissent. People simply aren't built to accept massive changes like that on a whim.
I think it makes sense not to choose Leliana if you support the Circle system, in some form. But just because radical changes cause dissent? I'm not sure. Change will always cause dissent, at any time it happens. Mages are already living outside of Circles during Inquisition. And as far as the race stuff goes, well, racial equality is an unpopular idea in Thedas, certainly. It was unpopular in America, as well, yet changes to legal (and, in some cases, religious) rules occurred, often well before public opinion was there. I'm wary of being more specific.
That being said, they keep everything about the new Divine vague and positive. You'll probably get a result that satisfies you, perhaps with some dead political or religious dissidents, but Dragon Age games train you not to care about those. (I think that's a little contemptible, but...) At any rate, I don't know how pro-mage freedom people get Vivienne, or how people opposed to that get Leliana... stop being so agreeable in companion conversations, I guess.