Right now, the bombers have 1 wing of Dragons and one wing of Manticores escorting them. What happens is that the escort quickly takes out Beta wing, but since Alpha has better ships and two of them have ship-guardian-threshold SEXPs for storyline reasons, the escort is unable to effectively engage them. This wouldn't be a problem with retail AI, but since I'm using Fury AI they very quickly tear the bomber wings apart.
There are a couple solutions to this; what you want to do is allow the shivans to neutralize the friendly fighters' combat capability without destroying them. When the friendly fighters hit their guardian threshold and invulnerability kicks in, you can:
1. Destroy their weapons subsystem (rather obvious to the player)
2. Degrade their AI class (simple, also somewhat obvious)
3. Swap their weapons to weapons with identical appearance but worse stats (a pain in the ass to set up, especially if the player can configure their loadouts)
4. Set a sexp with a high repeat count that will continuously set their weapons subsystem strength to a low value (I'm not completely sure if heavily damaged weapons subsystems inhibit the AI's ability to fire like they do the player, but if so, this is probably the most realistic solution, and easy enough).
edit: and it appears that when I replied to your post, I deleted your edit without reading it.

Still, I think some of the ways I suggested (particularly 4, if it actually works) are worth considering.