From the roleplaying point of view the agnostic or atheist option has immense potential: the middle age set that is the base for D&D implies that being doubtful about deities or explicity don't believe in them is something anyone would dare to think to be open with.
To see how the various believers react to [agnostic]/[atheist] dialogue lines would be interesting.
But just like some remarks from the banned one it could be a very inflamatory and divisive material. So I think it's best to follow the rules (also because there are some interesting deities in DnD, and the variety of them allows to really surprising character backgrounds).
I do agree with the user that stated that for specific races, like Drows or Thieflings, there should be the "recommended" deity to follow.
Keep in mind that atheism doesn't have the same meaning in the realms as it does in our world. There isn't anyone who doubts in the existence of the gods, or who doesn't believe in them, any more than there are people who do not believe that rocks fall downwards when dropper, or that the sky looks blue on clear days. They are a known, quantifiable fact of the world, and only the deblitatingly insane do not believe in them. It would be like not believing that cows exist, when you can go to market and see them in front of you. There is no doubt and no question here; it is overtly true and everyone knows it.
Rather, in the realms, atheists are people who, for whatever reason, do not believe that any of the gods are worthy of giving thanks, acts or deeds towards; that none are worth respect or worship, and who makes an active choice not to do so, and also (and this matters), to deny the gods any claim to their deeds and actions. There are no casual atheists; even people who don't actively worship a particular god still know, as factual truth, that they exist and that they have power; a farmer may politely ask Chauntea for good favour when sowing crops, or thank her for a good harvest, but that farmer doesn't actively worship her in any direct way... it's still sufficient. Even people who live their lives and never really think about the gods will generally still act in ways that some deities can take as worthy action. Being an atheist is something you've really got to dedicate yourself to, ironically, more than passively acknowledging various deities well enough to keep yourself out of The Wall of the Faithless, which is where all dedicated atheists end up. It's not nice.
Not to say that it shouldn't be an option, but it's a big, big deal, because it means a lot more than it does in our world.
