The easiest way to do that section is as follows (easy even on hard using this technique);
Before you drop down into that prison bit, use the mavity gun to blast down all filing cabinets, boxes, tables etc into the lower section (iirc, you will need to blast some cabinets up the stairs then over the railings).
Once you're in the lower section, you basically want to make a little fort in the room with the armour / health machines. Use filing cabinets / tables (also get everything from the other rooms in that section) to baricade the two side entrances. Put the tables so that one part makes a wall, and one part is on the floor, so you can then put boxes/filing cabinets on top of the bit on the floor to hold it in place. You should have enough objects to ensure no soldiers can enter your fort.
iirc there's 3 guns, and the scenario won't start until the 3rd is picked up / put down.
Put two of the guns down and barricade them in so they can't fall over. As soon as you put the 3rd down, either get in a corner, or inside one of the alcoves you took the guns out of.
From here, the guns should take care of everything.
If a gun falls down, pull it in with the grav gun, which will autonatically put it the right way up, then place it back down.
Jump out with the shottie (double blast if on hard mode) every now and again to take down and enemies if you need to, and have your crowbar erady for the man hacks.
nova prospect is one of the greatest levels / chapters in gaming history
