While I would adore doing the City Defence mission, the DD isn't designed for such circumstances, Asymmetrical warfare means nothing if our foe is basically numberless.
Our best hope would be using Hearts of Darkness and Carrier Pigeons to help with the evacuation. Might be a good idea to send Miller there as he's not exactly going to be skilled in combat. Heaven's Devils and the Metal Gear is going with Big Boss to close the wormhole.
The City Defence definitely will have to be a fighting retreat, we are not equipped to hold the line. Peace Day and Little Boom might be suited towards this operation. While I might like the idea of using the Lords of War to help with the city defence, we will most certainly need to defend the base, if one zombie got on, then it's more than likely that we have multiple zombies on the way.
Though the Supply Guys might be good for the purpose of Base Defence as well.
Though we do have the slight problem of our child soldiers and whether or not we arm them. I mean, this is Eli, so chances are he's going to break into the armoury anyway.