Since this thread has been resurrected, there might be a way to kill certain gods before they became gods, such as Cayden and Iomedae.
If you have a party that's hell-bent on killing a god, send them on a quest to search for the Scepter of Ages. By making the history check, they could technically go back in time before Iomedae, or Cayden and others, was a deity; say when she was just a babe in a crib. They could easily kill her then.
Of course, this opens things up to all sorts of bamboozlery. If there were a plot to kill a god, would said god know about it? Could they also travel back in time to protect their non-deific self? Killing them before they became a deity would have some serious repercussions on the future to be sure.
But that's the only way I could think of for players to feasibly kill a deity without outside help.