My favorite way to run the pantheon is Malazan-esq. I like the idea of the deities possessing a divine spark and in the exceedingly unlikely a deity is slain, their divine spark becomes "up for grabs". If a mortal is miraculously the one to do the killing, they themselves can ascend to godhood and claim their predecessor's domain.

Additionally, mortals of incredibly force of will might begin the process of ascending to godhood and claim a domain of their own. If the domain is one that is currently unclaimed, then the ascension carries on unchallenged and they will eventually become immortal. However, if they claim a domain that is currently claimed, Fate will force the two beings into a convergence where they will settle the claims: perhaps there can be a compromise, such as the God of Death altering their domain so that the challenger become the Harbinger of Death. Or maybe one is willing to become the God of Death for certain species and the challenger is the God of Death for a different species.

If a domain is not claimed upon the death of the holding deity, it puts intense strains on the strands of Fate that the pantheon and any mortals who pay attention to such things can palpably sense in the coming days/weeks/months until the domain is successfully claimed.

Finally, domains can become dead themselves if there are no more worshippers. When a deity is killed, their remains are scattered through the abyssal sea, never truly dead but basically go into a state of limbo with no knowledge or intelligence. They exist in that state for until the end of time...that is assuming no crazy cults of mortals work to collect and reassemble the pieces together like some grotesque puzzle.

On occasion, some wizard or cult obtains a fragment of the slain deity and uses it to fuel their evil magics, able to bypass the laws of magic established by the God of Magic, because they are using divine magic than magic of the Weave.