I'm not seeing the OPs suggestion that the PC cleric is "replacing" the deity (in other words, the other creature ceases to exist or is no longer divine)... but rather that the PC is absorbed into the deity and becomes one with it. Sort of a "collective unconscious" of all divine beings ever to rise up under a specific domain to become one with it. That in itself doesn't bother me at all, especially if you don't like to think of "gods" as specific individuals. Yes, there are certain settings where the gods are just people who can plane shift, have almost infinite power and not die from natural causes (like the Forgotten Realms gods)... but in other settings (like Eberron) the "gods" might just be concepts and having your spiritual essence become one with the concept would make sense and be fine.