I definitely agree that you shouldn't conceed victory points for a fighter wing when you're going to conceed even more victory points when you lose the carrier - that's just unfairly victimising ships with launch bays instead of guns.
However, it's also pretty clear that someone shouldn't be able to hide one flight and concede no victory poitns because you can't wipe out the wing. (a shadow fighter flight from each wing not jumping in, for example. Not sure If that's a possibility, but it's a good illustration, anyway)
If you wipe out a full wing of fighters you should get some credit. I think there should be more carriers as well, but in small patrols I see nothing wrong with the idea of a patrol boat with a couple of flights of fighters as escort. The problem is how to persuade people to buy a carrier as the points value goes up....
I really like the 'independant wings die first' approach; it's simple, you can't cheat it, and once you're at a priority level where you have a substatial number of capital ships at your disposal, it encourages you to field a carrier (something you don't often see in most races) rather than umpteen fighter wings.