About the difficulty of that mission - I would say it's mainly a case of how the player handles the Osiris. Dogfighting against fighters is a struggle due to the widely spaced primaries, and its shields aren't particularly strong, or so it seemed to me. I found that keeping close to the Karakius whilst under attack by fighters or reloading increased my survivability. Provided you time your reloads, you'll have enough torps to lessen enemy capship beam fire sufficiently for the Abydos/Marathon/Karakius to survive, and be able to complete the mission (imo....)
Other aspects of the mission probably don't need altering (apart from the extra bugs you raised).
Actually, I should also mention something else I noticed. I tried launching torps at the Pandora's front upper beam turret after it jumped in and began decelerating, but the torps flew through the turret and had to turn around inside the ship's hull to catch up. I think they eventually caught up and destroyed the turret or inflicted some damage. Seemed odd; is there some kind of sub-system/turret invulnerability tag enabled on the NTF capships?