I was defending the west entrance when I noticed a message about someone being killed to the south. So I sent two guys north and two guys south, since I had already killed most of the mutants coming from the west. At least enough that they were no longer a serious threat. Anyway, when I got to the south, all of the defending ghouls were dead. Up north, there was only 1 left. I killed the attacking mutants up north before they finished off the last ghoul. As for the south, I had sent both of my characters up on top of the church, and put them prone when they started to get in site of the enemy. Once there, I popped them up and discovered that there were about 7 mutants right beneath me. Well, I had an H&K shotgun and one of the other grey ones, so I had them both fire a burst into the attacking mutants. I was quite happy when between the two of them, 4 of the mutants died in one round! The remaining couple of attackers started to retreat and I killed them the next round. At that point, no mutants were within range of shotguns, so I switched to my rifles (M1 rifles, I think) and started taking shots at the mutants that were further away, making sure to duck down behind the wall after each round to avoid taking damage from the Miniguns.
Eventually, I managed to kill off all of the North and West groups, so everyone headed down South and cleared out the rest. I was also quite happy to discover that many of the slain ghouls were carrying sniper rifles, so my whole party now had sniper rifles, which helped when clearing out the rest of the map. Once you defeat the attacking groups, things get a little less hectic and you can proceed to clear out the remaining super mutants and kill off the commanders at your leisure. Still some tough battles, but at least they're not storming the town.
One thing to be aware of is that I played the mission in Turn-Based combat, as opposed to the pseudo-real-time mode (which sucks, IMO). Popping up and taking a shot before hiding again doesn't work very well in CTB mode, so it might be more difficult. Another thing to note is that I didn't pass the mission with complete success, due to the six or seven slain ghouls. I got reprimanded for not protecting them. Anyway, I figured by that point that it wasn't worth it to spend four hours replaying the mission just to avoid a partial reprimand. Besides, who needs a few more ghouls anyway? Heheh....