Disclaimer: This is based upon a rule set where the death of a sovereign is the end of that empire.
From the lore, the player character is a channeler, a magical being of immense power and one of the few with the ability to wield magical forces. As we have seen in the beta, you have two magical units: mana of the various elements and essence. Essence is currently only used to convert the land into the type livable according to your chosen faction.
Currently, when a sovereign is killed, that empire vanishes in a flash. I am suggesting altering this instant vanishing into a decay over a number of turns. Essentially, as long as the channeler is alive, their essence remains bound to the land maintaining it. Upon their death, it is no longer bound and the land returns to being neutral/wasteland/barren land. During this period of decay, the population of the city falls as people flee the dying lands, broken spirits because of the loss of their supposedly immortal sovereign, or some such reason. It will also allow an opportunity for the player or other AI sovereigns to claim the cities by using essence to re-imbue the land and save it. The benefit of this would be acquiring a city that is already developed without risk to military units or damage to the city itself.
This is kinda inspired by a line I remember from an old King Arthur movie, 1981's "Excalibur". When Percival goes to retrieve the grail he is asked a question: "What is the secret?" He replies, "That you (King Arthur) and the land are one." The land mirrored it's king.