It is actually possible to have the mothership intact for some of this battle but it will get disabled at some point. Mount the most long range scanner that you can get onto a fighter that has missile slots; fill these slots with torpedos. Keep an eye on the scanner and when a group of greys comes into view perform a missile attack on them with the fighter ( only have one torpedo turned on, you don't need to hit them with more). The torp will destroy the entire group. Slowly move the mothership towards the trade station ( I managed to dock here and resupply ). When ready set out towards the MSF station following the same routine. If you have done it correctly you should be able to get off a last torp at the greys near the station that will destroy most of them. Your mothership will now help in the fight.
Good luck.
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