First, get rid of all the fighters. Then, make a pass at the Dorkathi that's sitting near the depot - go in with your mass drivers, swing to the side, and hit it with side and rear turrets as you pass. Should be enough to take the transport (and its flak) out of the picture. Keep the engines on full as you go, and you'll soon be out of range of the flak from the depot (around 10,000).
At this point, sit around and wait for your shields to come back up. Depending on how depressed he's feeling that day, Doomsday (assuming he hasn't already bailed) will sometimes go in, and have a 1:1000 chance of destroying the station. More often than not, he just ejects and moans at you.
Eventually, your shields will come back up. Face the supply depot. You'll find (you might need to close in slightly), that you're still within range to get a torpedo lock, but the flak can't hit you. Once you achieve the lock, go to full thrust, and make a beeline (well, as much as a Broadsword can) to the station. When you hit around 3,500k - 2,500k from the station, launch the torpedo, and pull up hard. The flak won't be able to hit the torp at that range, and you can sneak up and over the station. The result: One torp hits the station, and you're moving away on the other side at 320kps.
Once you get outside the range of the flak (you'll notice the sky is suddenly a lot less red/orange, even while your VDU isn't showing any range info), turn back around and come to a stop. Repeat the earlier procedure of locking on at range, waiting for shields to come back up, and then going to full power. The second torp will kill the station. After that, if you feel generous, tractor in the more-than-likely ejected Doomsday, and start the journey home.
