God dammit, finally. I god damn did it. I'm going to post what I did so maybe if anyone else has trouble with this part, they can maybe get an idea on what to do here. I'm talking about the part where Freeman runs into the lobby, the door shuts behind him, and soldiers start coming in through the ceiling. Now, I did this on Hard - I'm not sure what exactly should change, but it should be easier for you if you do it on a lower difficulty. So this should help anyone.
This may have a few spoilers, so I'm going to make the text invisible. Just highlight it to see it.
So from the previous puzzle, you should have picked up the Tau Cannon, also known as the XVL1456 - which is printed on the side. Run into the lobby behind the one crate straight ahead, so you should see the soldier come down. Immediately start firing single shots with the XVL1456 and try to land a headshot, he'll die within a couple of shots. While the other soldier is still sliding down, kill him just like you killed the previous soldier.
Now, sprint towards the H.E.V. Charging Unit, zig-zag if you have to, crouch down, move side to side and start charging up to get whatever health you need to. Get your crossbow out - hopefully you have one. One soldier should get behind the desk, kill him. Two more soldiers will start coming in through the roof again. It's different each time, but the one should come down from the left or right - crossbow 'em. Then the other should come down from the opposite side, kill him too. There should still be one guy behind the desk, kill him.
Now start tossing grenades over at the locked door on your left. It will open and soldiers will start coming out. Whatever ones don't die from the grenades, finish them off with the Magnum. Now, stay away from the skylight. There should still be two soldiers on the roof. Get behind the desk, some crates, wherever you want and take them out. After you kill them the door you came in should open back up. Congratulations.
I love this game, but what really irked me is that one of the hardest parts so far for me has some badass music playing - but the area is so damn hard that you die so many times and it ruins the moment. Still, I love this game so much. Now onto Surface Tension...