beams and shooting at fighters

While the iron is hot....

My big beef, from a recent game, is with the 
inability of ships to engage non-attacking 
fighters. Here's the situation: Landing assault on 
a planet. Assaulting player is losing transports. 
But his fighters (having wiped out the 
defenders) are utterly safe because the 
defender can't fire at them if they don't attack. 
He says to me "Why don't I put my marines 
aboard fighters since they're invulnerable?". He 
was being facetious, but the point was valid. 
Since ADFC is uncommon in FB designs, and the 
defending fleet had none (mostly small ships 
like CVs, FFs and DDs), they were utterly unable 
to swat the pesky fighters flying around. They 
could kill any OTHER object on the board.... 

I wonder if there is a good way to address this.