Hey guys, it's me again ! The one who is trying so hard to succeed its mission objectives that I get stuck in the end
I did manage to destroy all those pods. On the first "staying alive" try ; on every other tries I got killed because 1) I had virtually no wingmen, since they all had their Weapon subsystem destroyed, and 2) not enough energy to take out all those transports, but i did my best and sacrificed a bit too much hull everytime..
Anyway, to have a bit more of survivability, on this particular run I chose to ignore some of the transports and focus on the fighters instead. I kind of figured out that it was all scripted, and that no matter how many transports dock, I would get to see the "pods escaping" part. In particular, I chose to override Shields instead of Secondary ; I quickly destroy the Horus that attacks me, and then i just went for the pod with all the ballistae I had. Prior to that, I had also weakened them just enough to be at 20% hull for most of them (heading out to fighterbay right when the lady pronounces "something something FIGHTERBAY")
Destroyed them all. Then the mission got stuck.. No "hurray you destroyed all the pods"
I had to restart it all, and by chance, it turns out on second try I wasn't able to destroy them all.
I guess those pods are supposed to have a plot armor, but could it be done even more impossible to catch them? If I didn't have ballistae I'm quite sure I wouldn't have been able to catch them, for instance.
Also, on 1st try as soon as I heard about fighterbay, I headed there ; when the pods came in, I figured out they had to be destroyed even though they were green, so I destroyed one of them before it turned red. Didn't end very well, got judged in martial court