If the supernova were a torpedo with faster tracking and speed, wouldn't it be good against fighters? Also, I don't know how the issue with Capital ship shield generator hard-points and explosives will be resolved. If the blast radius is too big to encompass the generator hardpoint, then it might get ridiculous (the explosions could be used to kill fighters flak-style).
A touchy issue balance and player-attitude wise. I would personally rather increase capital strength than nerf the supernova, but if it were to be reduced in usefulness, I'd reduce the damage.
Edit: apart from changing weapon numbers on bombers (player wipe needed?) I don't know the best way to reduce their "anti fighter" strength. Perhaps the fire arc of the supernova could be reduced, so it can't just fire across in a joust at wide angles. But that might affect gunboat-bomber combat.
Most bombers don't seem good against fighters, apart from the catamarans and the Taiidan. Those are hard to hit and are good in dogfights. The rest however, are large, sluggish and rely on very lucky hits with a supernova to win combats.