One of the features that we expect to get into Elemental Beta 1B is the Sovereign "hide" option.
Right now, if your sovereign dies, the game is over.
The downside of this, long-term is that in single player, you'll have players figuring out ways to assassinate AI players (i.e. crazy amounts of AI time will end up getting spent countering assassination strategies) and in online play it'll be "kill the sovereign".
With the hide option, when the sovereign is on a city, the player can choose to hide the sovereign at which point his player piece is no longer accessible. If the city he's in is taken, a dialog comes up and tells you that your sovereign has successfully fled to the closest city.
But at any time, the player can also have their sovereign come out of hiding and the player can then have them go do their thing, give bonuses, cast spells, etc.
The objective of the sovereign unit isn't that you are supposed to have to worry about protecting him but rather that the player can "gamble" it all if they choose in the form of making use of a single unit that is extremely powerful (potentially) but also could spell doom if that unit actually gets killed.