You can do a PhysicalDamageAsDamageDealer modification on the enemy ships, but this sort of thing isn't possible. Your mini ships are going to be anti-everything, there's no way to make them only attract missiles.
You can almost turn fighters into decent missiles by giving them a very short range and an equally short range magnetism effect, so they will get themselves sucked into the enemy ship, dealing damage when they impact. I have a working example of this in the SOA2 mod with the Borg version of a hangar bay.
It would be messy, but such a thing is the only way I can see to do real point defense and such, missiles are just particle trails in Sins, not something you can specifically act against. If you didn't mind modding strike craft out of the picture, you could rework all the targeting in the game to have missiles attack strike craft, then make them be the countermeasure.