One of the editors over at Bit-tech has ediorialized about the lack of support for atheistic dialogue responses in Dragon Age: Origins, which is something I've surprisingly never really given any thought to. He uses The Urn of Sacred Ashes quest as an example:
It all started with the mission where you have to collect the ashes of the prophet Andastre from an ancient temple, with the overall aim being to use the reputed healing power of the ashes to save the life of a nobleman. I sought out the ashes with no problems or qualms, not really concerned with the religious significance of my characters actions in any real sense. In fact, I was treating the ashes not as a holy relic but as just another magic item to be collected and used. If a pinch of ashes from the remains of a deity's spiritual wife actually restored another man to life, I think it would be difficult for the populace (particularly the protagonist, who sees this firsthand) to discard the religion's beliefs.
The key word there is: magic. Ferelden is a world where magic definitely exists and is used regularly. The Chantry god though, is not. The Maker never comes down himself to give you a +2 Sword of Archdemon Slaying, he acts in mysterious ways instead. There are lots of references and legends about miracles and holy powers, but who is to say that these aren't either natural or magical phenomenon? To me (and my character) those options seem far more likely than supposing that the Chantry's religion is correct (and that the Elvish and Qunari religions are therefore invalid or possibly forming a larger, less possible pantheon).
My character wasn't touched spiritually by the task and I personally had found the temple to be little more than an over-long dungeon grind with some obvious, predictable puzzles tacked on the end so no holy revelations there. The nonchalant answer seemed even worse though, as while dismissing the ashes as nothing but ashes may have distanced my character from Chantry doctrine in some regard, it would have also passively reinforced them by confirming them as Andastre's ashes more blatantly. The line offered wasn't "I got what appear to be magic ashes while remaining unconvinced about the validity of your convictions", its "I got the most holy proof of your God, but I'm too cool to be moved by that fact."