Good point, although the destruction of the Chantry wouldn't really need to affect peoples faith in the Maker/Andraste. For example, a revelation like the Chantry use the side effect of lyrium to control the Templars would probably come as no surprise to most people in Thedas, but it would certain shake up remaining loyal Templars/Seekers/etc.
*Edit* Or is that kinda what you mean by a political upheaval? Stuff that only effects the Chantry due to their own actions, like the lyrium thing etc? I'm still half asleep, lol.
LOL I suppose the lyrium addiction thing would be political (I was thinking more "Andraste was a mage" kinda thing for "sacrilegious"). And cool! Heh heh. But then, if most of Thedas doesn't give a crap about the templars, like Cullen seems to think, then I also wonder how shocking the lyrium addiction reveal would be.
Whatever it is, I'd love to see the Chantry on the ropes. I find it unlikely that we'd see a total collapse of that institution, but seeing it reorganized, or seeing it threatened by the rise of the Black Divine or something like that. Like, suddenly dragon cults pop up everywhere, and the common people are joining in droves (like end of the world cult kinda thing), and the Chantry is scrambling against this threat to its supremacy and piggy bank. Something like that would be cool.
You know... given Mark Darrah's very particular tap dancing on the subject of the Inquisitor being "against the Chantry" in his/her goals, I almost wonder if that's the sort of things we're headed for.