We don't know how many people in Andrastian society are agnostic or atheist.
Tumblr's search engine is terrible, so I probably can't dig it up, but David Gaider has said that atheism basically doesn't exist in Thedas, anymore than it did in 15th century Europe. Still this argument is going to start going in circles. Basically, I think it's funny how you always call humans Andrastian humans. I think you're the only person on this forum who uses that word in any context other than contrasting the City Elves to the Dalish. And even then, odds are good it's you anyway. 
Considering how Oghren points out that a rich wall of lyrium is changing everything in the temple, including the ashes, I don't see why it would require denial for someone to believe that there isn't a Maker or that there is no higher power.
Lyrium does not do that, and we have no reason to think it ever has. Lyrium isn't a catch-all, do anything phlebtonium, it has specific and well-defined properties, none of which come close to explaining even half of what we saw in the Gauntlet. Not to mention the complete lack of any such magic in the Deep Roads, which also has Lyrium out the wazoo.
But this isn't really the right thread for this debate, so I'll refrain from continuing.