You would add a file called sgreenrate-wep.tbm to your data/tables folder and add:...
Wouldn't do it that way, just work on the Weapons.tbl itself, far easier.
For the beams, as Mars said, just change the SGreens fire rate, damage, whatever so it fits. Just search your weapons table for sgreen, you should understand what those values are for (if not, just check the wiki). For the Anti-Fighter-Weapons... how about some new stuff? E.g. for my campaign, the Capital ships AA-defenses are some kind of machinegun with a little Mace-effect (gave them a little FOF though, without the inaccuracy they were too powerful).
Or replace the turrets (primaries) with some kind of homing missile (secondaries). Use your fantasy

Edit: The weapons table is in the fs2_root.vp (or something similar ^^). If you don't know how to extract it, just tell me, I can upload one so you can simply download it.