I am aware of the fact that in-game it would be silly to deny the existence of gods, but I'm worried (and I think legitimately so) that this reflects the views of the developers and is an expression of such, rather than a purely IC thing.
don't worry, it isn't. at least of myself I know quite well that I'm anything, but a religious person.
I don't know about the believes of the others, but I'm very sure that is has little effect on the work on this project.
actually, you don't have to limit yourself to the choices ingame, either.
for example you may play a character that isn't atheist (i.e. doesn't deny the obvious existence of gods), however doesn't follow a specific one either, which would probably fit a very well educated character that doesn't fail to see the relation between the gods