In practice news, "The Queen" is a ***** of a mission, even if you're an RTS god. I worked out the perfect dozens of commands in the first few minutes to have cruisers picked off while I take out that under-engine beam turret on the destroyer that rips the corvette apart, and can take out the beam turrets on the Sobek and take it down before the Knight even reaches 90%. Yet no matter what I try, by the time the Sobek goes down and the destroyer is just limping along, the crossfire and enemy fighters are suddenly dialed up to eleven so that within 20 seconds all my wingmen are obliterated, leaving me as the only slow, defenseless target to get pummeled from 95% down to 0. So essentially, I can destroy all of the capital ships, but surviving is another issue.
I cheated and got through to the end to read debriefing, and it mentions that the Sobek was not a priority in recommendations, even though they still gave me a pat on the back. So my next strategy is to try taking out the destroyer before the Sobek, since it drops pretty quickly once all focus is on it, and that's where all the enemy fighters come from. I've been neutering the destroyer by taking out its Weapons subsystem after the beam turret, so it becomes a sitting duck. It may be that the issue is that so long as it exists, the fighter wings pose the biggest threat. I will give that a try and see if the Knight can just tank the Sobek's yellow beams for another minute.
UPDATE: Okay, a bit more micro-managing of wingmen made this more feasible, as well as putting Beta in some Herc IIs. Calling in reinforcements as soon as you get them is still a must, as I believe what's happening is the Sobek's flak begins to tear up fighters since by that time in the mission, it's right on top of the Knight and we're forced to fight in the middle of a flak field regardless which of the two remaining ships we choose to go for. I got all objectives completed though, and then at the end the Knight took "severe damage" from a stray bomber. What a headache of a mission this is. Hopefully we can get it in one go on stream this Sunday.