This mission was crazy! (may contain some spoilers...but you wouldn't mind i guess ^^)
First off, I always skip this auto-flight-stuff, don't like it - at least at the beginning to make ridiculous amounts of money. Was fun while being hostile with MSF
All Pilots have rank 4 ship, I prefer the Puma, it's more manoeuvrable. Now one thing you should have, there is a talent from your main guy. 1st rank gives you 2 charges of being nearly or highly invulnerable for 30 seconds (ah just checked, it's called "Sixth Sense"). I guess you learned it? Was my main survival skill for this mission and:
in any case you'll lose Ternie (temporary/scripted event crap) so either give her a ship which you can afford to be wrecked or strip at least off her better equipment. I was 'slightly' pissed, as she had in my game 2 of these 200k sniper laser
and all of the other stuff you can get from your FTU talent
So i restarted and changed some stuff, but this made the mission even harder...but finished like 30 minutes ago.
The 'new' guy leaves right after the fight is over, so don't plan to change his equipment. He'll do fine.
The only thing that helped (besides your 'sixth sense') was as soon as they ambush you...click like a maniac thru all available skills - but I think you've done this too. If you have short-range-missiles, they'll come in handy. Right in front of your mothership shows up a butcher, this guy is ridiculous evil paired with all the fighters around. If you have BFG's (big f*cking...) on your mothership you may pray that they hit em hard. otherwise he mowes around with his Plasma(?) guns.
Used a main save right before the event, and a lot of quicksaves
In any case, it's just pure luck....but if you survived the berserk ambush (2 capital ships + lots of freaking stuff) right after the aliens, you shouldn't have that problem with these guys? Problem with the berserk was only starting being the target with your mothership and all your fighters still in yer bay.
(as said, you 'll lose 2 guys after the mission, the new guy leaves. Don't know yet if he come back and your next mission 'll be the search for Ternie)
hth somehow...