It's possible that the distinction between Atheism and Agnosticism would be irrelevant in game terms, as both are people who don't have any gods in their "worshipped" list, but I think there's a way we can make the difference mechanically interesting.
Religious philosophies encourage the worship of gods or a specific group of gods (possibly only one). There's going to be a lot of variety here, depending on the gods, and how well people understand them.
Atheist philosophies disapprove of worshiping gods, and consider membership mutually exclusive with religions proper.
Agnostic philosophies neither approve nor disapprove of worshiping gods, and pursue dual membership adherents from both religious and atheist philosophies.
Atheist philosophies will naturally clash with any religion, even if that religion is ambivalent towards them, while agnostic ones could get along with a religious philosophy, if that's also withing the religion's tolerances.
This could get more fine grained, if that level of abstraction becomes unacceptable.
Atheism could be further broken down into the ideas that "the gods do not exist," and "worshiping the gods is morally wrong," (Anti-theism?) but that might be more fine grained than necessary, depending on whether there's a mechanical difference between the two.
If we draw a line between these last two, there are two ways that I see to make them distinct: First, a good round of smiting will bring around all but the craziest of Atheists, but is likely to have the opposite effect on Anti-theists, especially if they are a highly non-violent sect. Second, Atheists are going to be very rare in a world where the gods are highly visable, while Anti-theists like McConspiracy, are going to crop up a lot in such a world, especially if the gods have humanizing flaws, or are capable of being harmed by mortals.