Perhaps the Terror Stars could have some sort of Drone technology?
Everyone likes to use the example of Aircraft Carriers and while they do have some weaponry on board, they do have a whole bunch of planes! Along with the Terror Start line of techs, put in a tech where the Tstar would be equipped with drones so that in the event of a battle against a lone fighter it won't be completely dead in the water.
The drones however would not be enough against a Frigate or Cruiser, just enough to get through a few fighters.
The above idea makes me think of Return of the Jedi when the Rebels attempt to go destroy the new Death Star. While the Empire has a butt-load of Tie Fighters defending it (for those pesky X-wings), it also has a huge amount of Star Destroyers with it as well. Without them, the Rebels could take their frigates and destroy the Death Star much easier.
It would need some balancing to get it right, but I think adding a few drones would fix a lot of issues about worrying about the one fighter. The drones can also be destroyed and you would essentially need to purchase new ones or run out.