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Or there never were any gods to begin with, just religions that had cropped up over the ages based on false mythologies.

As for creating one, I would go with something primal and elemental in nature, one that wants to 'change the face of Athas forever', but in it's own twisted and limited vision. Even a water or rain primal force that would see nothing wrong with drowning it's followers in torrents of water. It could even be actively duping it's prophet with false promises of bringing change to the world to the benefit of the people when in reality, it simply wants a greater share of the Athasian pie so-to-speak. You could go with the basic fire, earth, air, or water, or the old-school para elemental silt, sun, rain, or magma ones. A primal force of rain that envisions one great endless storm of destruction over the face of Athas . . . now why does that sound somewhat familiar? The revelation to the poor prophet of such a being could be very sorrowful ("You just don't understand me, Prophet. I'm a being a pure fire . . . all that I am, all I know, all I will ever be . . . maybe if you burned, for a little while, you'll understand . . . you will all understand!")

The prophet of a non-existent deity based on ancient histories could be interesting, but I'm at a loss as to how to culminate such an idea (meaning, how to eventually expose that no such being really exists in a way that works well). Post exposure however would have one manically depressed and likely quite vengeful former prophet that could lead some serious rallying against other presumptuous claims of divinity (thinking of Abalach-Re's trumped up religion of Bad'na if you wanted to have a city already in shambles ever rise up against it's own Sorcerer-Monarch) or even strike directly at one of the SKs who claim godhood like Hamanu or Tectuktitilay only to be quashed like an insect be powers that, while not necessarily divine, are no less potent on their own turfs.

As for actual gods, you are on your own for that. I'm too much a purist for going that route myself, but there's nothing stopping you from dragging your players through the Astral to revive a dead god and bring Athas it's first truely divine being to shake things up. I don't think any current existing deities would really fit the bill for any avenues I can think of, since most of them are niche gods that are part of a collective pantheon (A god of this, or goddess of that would seem rather out of place as the only god on the block on Athas). Think more along the lines of what a monotheistic god represents in the grand scheme of things.

Introducting Gods from other settings is certainly not for me, but to each his own. Restoring the Gods to Athas, or Athas to the Green Age, seem to be common themes for Dark Sun. Though I would argue that they are already becoming cliche', kind of the Athasian version of "I won D&D".  For me anyway, these destroy what is unique and cool about the setting. After completing either of these epic quests, Athas becomes just another generic fantasy world, albiet with a slightly more interesting history. I have also had three of my players request to play divine characters, I just don't see the attraction, other than playing something forbidden I suppose. It makes me wonder, how many people would pick up the Forgotten Realms campaign guide and decide to run an epic campaign where the PC's run amok killing the Gods and destroying the planet?

Anyway, I don't know if anyone has brought up the possibility of having the PC's becoming the New Gods of Athas  after they reach 30th level (how is that for an Epic Ego trip for your players). After all, the old guys had their shot, and they didn't do such a fantastic job, why give them a second chance to F it up. Not to mention the luke-warm reception they would likely recieve from your average Athasian citizen, given their well known failures. You could even keep the campaign going with the continuing saga your PC's as Gods if you wanted. Lot of work to do creating their realms in the Astral sea, figuring out their dominions, fighting those who would see these fledgling Gods destroyed. 30-40th level = God Tier

The primordials step up and take the place of the Gods. It's been a while since they were young and destroyed the Gods. Maybe they've matured a little and now see promise in what they once considered insignificant beings?

Another possibility would be to have some of the major NPC's of the setting attain Godhood. There really is no need to have dieties everyone likes, or who are even devoted to the concept of good. What would happen if Borys has actually been working on attaining God status in his spare time between devouring sacrifices and playing shuffle board? Suddenly he takes to his new realm in the Astral Sea taking his minions with him. The Sorcerer Kings are left scrambling to replace him as Rajaat's prison begin to weaken, threatening to release him back into the world. You could have an Avignon (sp?) achieve Godhood to balance out Borys. 

What about Kalak? In my campaign he has been killed, but don't count him out just yet. He may have spent a few years sulking about his death, but Kalak is scrappy. Finally he has realized that his death at the hands of that numbskull traitor Tithian was a blessing in disquise. Kalak goes back to doing what he does best, being in charge. Having adjusted to the Gray, he has decided to take it over and make it into his own realm. He is currently organizing his new, and ever growing legions of the dead and plotting his comeback. Kalak the Gray, new lord of Death and the shadowfell, acting much like the Raven Queen, only not so nice. Now if revenants he created would manage to kill Rikus, Kalak could make him lead his new legions further into the depths of the Abyss. Is he a God? not really, but he is still a force to be reckoned with.

Above all else, do with the campaign whatever want, it is your game after all, and tastes vary.