This is true. And we never see (in game) any of the major characters insisting that they are doing their bad things in the name of the Maker.

...then again, Loghain seems to be about as close to an atheist/agnostic as you can get. But even that POV is one that is really very modern.

Although if you complete Chant from the Deep or free the mages, the Chantry does consider another exalted march. (I do wonder, considering that it's coming from the Divine in Orlais, whether you could consider this a further sigh of potential Orlesian aggression.)