I'm not sure that beefing up capital ships' armaments is necessarily the best solution to their vulnerability to fighters. It's not the worst solution either, mind you, since blob turrets are so pathetic, but it's not the best.
I think the biggest problem with capital ships is that it is so easy for fighters to create blindspots in their defenses, even if initial turret coverage is pretty strong. For example, the two AAA beams at the rear of the Sobek is a pretty strong deterant to attacking fighters, but once some brave/poor soul moves in to destroy them, that whole rear quadrant is utterly defenseless. Let's pull a role reversal, and put you in the Sobek's command chair. What do you do when your tactical officer informs you that your aft quarter has been neutered? You probably tell your engineering teams, in no uncertain terms, who will be neutered next, if they don't restore those AAA beams to operation. Of course, that's a lot of scripting (especially if you want repair rates to slow as more turrets are damaged, representing a splitting of the repair team's efforts), so from a meta-game perspective, it's not a viable option, except in the rarest of cases.
Aside from that, I'd also consider making a couple of the player's weapons a little less ridiculous. The Maxim really needs its range dropped down to between 1250 and 1500 meters, like the Prometheus S, so that you can fire from a healthy range, but not without fear of reprisal. On top of that, the Trebuchet needs to be targetable as a bomb. This would make it equivilant to an advanced Stiletto in terms of its turret-smashing capabilities. (i.e. You can kill turrets from beyond their range, but you'll need to fire off the better half of a bank in order to overwhelm the turrets you're firing at, thereby making them a slower and less attractive option.)
I suppose the solution you choose depends on if you want to beat the player with the whoopin' stick or the nerf stick. Of course, lately, when I've been building missions, I opt for option three, not making the Maxim or Trebuchet available. Don't like the Prometheus and Stiletto? That's just too bad, now, isn't it?