Successfully destroyed the Hades.
I tried to take some screens, but my system wouldn't grab them.
But for the curious, here's how it's done:
The Egyptos must have very high hull integrity in order to survive the Hades's beam barrage. The station doesn't begin evacuating until its hull reaches 75%, and I'd estimate that it'd need to be no lower than 65% when the Hades jumps in. On this particular attempt, the station got away with only 2% remaining, so the margin of error is very narrow.
The key to this appears to be aggressive bomber defense. I had almost 40 kills by the end of the mission, the majority of which were bombers. Hunt them down as soon as they jump in, and leave the fighters to your wingmen. The Lokis can only cause minimal damage to the station anyway, so the bombers are your priority.
Doing this slows down the pace of the mission significantly. Because the number of fighter and bomber waves are set, and certain events in the mission are triggered by how much damage the Egyptos has taken, keeping the station's hull integrity high gives you some breathing room to clear out new enemies as they appear and stay on top of things. For example, when the Leviathan cruisers jump in, you can order all your wingmen to attack them at once and destroy them quickly, since they exist primarily as a distraction and bullet-soak; knocking them out in a hurry frees your wingmen up to go after fighters and bombers.
Ignore the Roskva Hercules fighters that go after the Hathor. They won't be able to destroy the cruiser before it jumps out, and when it does, they'll retreat.
Toward the end of the mission, watch out for the waves of Hrid Zeus bombers that jump in. They arrive shortly before the Hades does, and can ruin your run if you aren't careful. Don't forget about Sneak, either.
When the Hades jumps in, order your wingmen to ignore it so they'll focus on the remaining fighters and bombers. Theta bombers will jump in right after the Hades does and cannot be given direct orders, so don't worry about them.
If the Egyptos survives the Hades's attack, clear out any remaining bombers. There may be an additional wave or two after the Hades actually stops firing, so don't slack off. The same goes for the Lokis.
When all enemy craft have been destroyed, order your wingmen to disarm the Hades. Theta will continue to attack regardless, so don't worry about them. Focus your attention on the missile launchers, because they pose the biggest threat to your wingmen. You can ignore the beam turrets, as they are difficult to destroy and won't fire again anyway.
Then it's just a matter of waiting. Theta wing and their tsunami bombs are the only ships that can cause any appreciable damage to the Hades, and while they'll automatically rearm themselves and continue to attack, this still takes time. In Last Stand, you have four bomber wings attacking the Hades simultaneously; in Blood of the Innocents, you only have one, and none of them carry Harbingers. You can't use time compression either, because it doesn't work properly and will cause your wingmen to do dumb things like crash into the Hades or each other, so just be patient. Eventually, the juggernaut will go down.
>Destroy Hades marked as clear in objective window
>At the same time, primary objective failed
Well fine, be that way.
There's not much to do after the Hades explodes except jump out, and you'll receive the same debriefing as before: praise for assisting in the evacuation, and punishment for jumping out prematurely, since the Egyptos was never destroyed.
This'll make the rest of the campaign very awkward...