I think that whole thing was pre-Qunari invasion. That must have been a serious, "Oh SHIT" moment for the Chantry.

I do find it interesting that Rivain is non-Andrastean--and has good relationships with both the Qunari and the Dalish--but so far, the Chantry hasn't gone after them. Maybe they're not big enough/don't have anything the Chantry wants at the moment?