There is no 'atheist Inquisitor'.
Your Inquisitor can express various atheist beliefs.
But at no point is the Inquisitor someone who identifies as atheist. If he even did, it would be on the agnostic side of things.
Inquisitor can be anti-Religion and deny the Maker, etc, sure.
But the Inquisitor is never outright antagonistic towards believers in deities just because they believe in deities.
This is one of those cases where your vision of RP does not fit the dungeon master's Bioware's version of RP. You had to get along with Cerberus. You had to be an agent of the Council. You had to stop the Blight. ..And you had to accept the responsibility of leading a population of people that was predominantly Andrastan. That's the story.
I wouldn't have been entirely opposed at there being an alternate form of that scene though. One where you can silence the song that is starting and give your own speech. However, this path might have had to work with the rest of the plot, and I don't think Bioware would have been ready to try such divergence.