To me a cleric without a diety makes a lot of sense, what wouldn't make sense to me is a cleric without a church (in the sense of a group of beings with similiar beliefs and common rituals, whether or not they have a building set aside for rituals). Dieties are commonly seen as deriving power from their church, which they then distribute to the clerics. What if the church was able to cut them out of the deal and grant the collected magical power directly to the cleric? For the cleric, being in harmony with the church's gestalt, or abiding by church law would take the place of the individual judgement of a diety.
These churches could either form on their own, or it could happen if the diety dies, gets bored, or disappears. (In my old campaign a conspiracy of high level clerics had in the past locked all dieties out of the prime material plane and took control of the combined churchs' power themselves. So there was only one church, and no dieties.)
Has anyone had clerics in a campaign without either a diety or a church?