Destroying the fighterbay won't really do anything. This mission is extremely frustrating, and the only way that it was completeable in FS1 is void now due to the big ship flag. I've gone through this mission a couple of ways in FS2.
1) Spam fighters yourself. Equip yourself with an Ursa with nothing but Harbingers, and your wingmen with Ulysses/Hercs. Have them cover you (or engage enemy while ignoring the Jotunheim) while you take out the station. When the Hades arrives, hang back from engaging it until the cruiser arrives, and then order every wingman available to guard it. The sheer number of fighters on your side will decimate the Lokis, while the Oorf fires on the Hades. I've always just done this until the Lokis are exhausted (it's 99 waves, but there's still a limit), and then had whatever surviving ships exist attack the Hades.
2) Spam bombers. Much less advised, but it can work sometimes. Ursas and Medusas work best here. Order your wingmen to all attack the Jotunheim, and simply the sheer number of warheads will destroy the Jotunheim quickly. The turret fire from your bombers will be sufficient to take out enemy Lokis, though you may want to give your bombers some anti-fighter missiles such as Hornets. The Hades half of the mission requires either guarding the Oorf as in the first example or disarming the Hades near the fighterbay and simply camping as the Lokis respawn while one or two wings work on the Hades.
Extremely frustrating, and I still wouldn't highly recommend the above strategies either; they're simply ways that I've been desperate enough to try.
