It is possible to be an atheist in this game. If my sources for the definition of atheism are correct, an atheist is one who rejects the existence of God or gods. A character in game can say that they believe in the existence of Laanx, Talad, Xiosai, Dakkru, and whoever else is considered a god, but deny that they are gods. Instead he or she can insist that they are just really powerful beings.
I think misotheism is too narrowly defined to be the appropriate word. Characters do not need to specifically hate the gods, even as they believe in their existence. They can simply be dispassionate about religion in general. It's a fair character choice, as religion in real life is always able to cause heated debates, and is a very personal experience. Not wanting to bring that baggage into a game is reasonable.
But I'm splitting hairs here. Whether someone chooses to role play an atheist, misotheist, agnostic, or simply just secular, the original quote is just a guideline. I look at those as simply assistance to get the new player thinking about their character. For me, the initial choices I can make when creating a new character are way too limiting, so I hardly bother acknowledging them, except to make sure they're not completely off the wall.
The wording might be adjusted slightly, but it would be hard to capture all of what one should be thinking about when choosing that religious option. As it stands, I don't see people who have had a bad experience with religion, or staunch individualists as necessarily bad people. I know one of the former, who is a very good fenki.
Edit:
I knew there was something else I wanted to write. Regarding Dakkru's revelation number three, I never thought that it meant that when a faithless character died, that was permanent. But I do think that Dakkruists would, in particular, have strong opinions regarding those people. The question is, when does one's spirit shrivel? I would say that death in Yliakum is only a corporeal death. I thought the 'all' in that last sentence, "All who die the true death are Yliakum's gifts to Me," was, in fact, all people who die the true death, but now I'm thinking it means all the faithless.
It is completely appropriate for this to be vague and left up to interpretation, that makes the differing opinions of the characters that much more interesting. If all we had was established dogma, well, you'd still have inter-faith debates, but not so much intra-faith debating.