My bad, fusion cannons. Silly words.
I know they're only AF within 4 inches, but outside 4 inches you have a reasonable chance to put at least 6 hits on a squadron (or spreading your fire a bit). 1s do pop up with alarming regularity.
When you consider there are Minbari ships specifically designed for anti-fighter duty, outfitted with fusion cannons cannons, with 4-6 dice in every arc, I'd be darn sure I made them use those weapons as intended. Throw dice at them at long range, take out 1 or 2 if you're lucky. If they close to within 4, take them apart (1 dice each on up to 6 squads).
If you've lost ships to fighters, you need to treat them as a threat equal to or greater than the capital ships lurking in the distance. I'd throw every dice I had at them, and rely on stealth to keep the capital ships missing, until the fighters were gone.