Okay, so this is what I have so far:
[ ] Ghor Province: Wormhole Assault
-[ ] Big Boss, Quiet, D-Walker
-[ ] FULL DEPLOYMENT 1st Co. "Heaven's Devils", 3rd Co. "Lords of War" 4th PLT, Metal Gear Sahelanthropus
-[ ] Screen Sahelanthropus, move hell for leather to the Wormhole. Use any surviving Soviet assets.
Self explanatory: Best of the best, with the Metal Gear, right at the heart of the enemy. If we're willing to risk Kandahar, we can put all of Diamond Dogs mobile assets (Lightning Raiders, Sheridans) on this assault.
[ ] Battle For Kandahar: Hold the Road
-[ ] Ocelot, D-Horse
-[ ] 2nd Co "Hearts of Darkness" 2nd PLT, 3rd Co. "Lords of War" 1st, 2nd PLTs, 1st Recon Tank Co. "Little Boom", 2nd Rocket Artillery Det. "Peace Day", 2nd Flt. "Chirp Chirps"
-[ ] Mobility is key, mobility means survival. Let the locals hold the line while Diamond Dogs sets up defensive positions (from foxholes and emplacements to mines and traps and everything in between), provides mobile support, thins out the horde.
Advisers to support and liaison with local forces, Lightning Raiders and Helljumpers support the Sheridans, staying mobile while they receive artillery support and the Little Birds provide spotting and recon. The objective is to keep the locals fighting as long as possible, and maybe drum up more.
EDIT: Added in what
@Shashenka pointed out about defensive works/positions. Hell, if possible, we should get the civilians involved in building defenses, ala Moscow's population in the fall of 1941.
[ ] Mass Evacuation: Afghanistan
-[ ] D-Dog
-[ ] 2nd Co. "Hearts of Darkness" 1st, 3rd PLTs, 3rd Co. "Lords of War" 3rd PLT, 1st SQN "Carrier Pigeons"
-[ ] Save as many lives as possible.
Self-explanatory. Rest of 2nd Co. deploys, even the spooks, to organize the evacuation via Black Hawk and Chinooks. The more civilians are evacuated or at least pointed at safe zones, the less zombies there will be to fight.
[ ] Mother Base Defense
-[ ] Master Miller, Eli
-[ ] 1st Co. "Supply Guys", Mbele Squad
-[ ] Hold down Mother Base, protect current refugees and any that may/will arrive.
Miller doesn't have to be on the ground to oversee the evacuation. He can oversee the missions from Mother Base while keeping an eye on Eli. The Supply Guys are though, so they can hold Mother Base. Besides, if units have to be evacuated, they'll bolster Mother Base's defenses.
[] Arm the Child Soldiers
Arm them and have Elia tell them the stakes. They're fighting to protect the refugees that can't defend themselves against a threat greater than warlords or PMCs.