The beam thing is actually impossible to change correctly with turret aiming constraints. I can't be bothered to find the info, but its been dicussed thoroughly on the Starshatter forum. (SS is a game in beta, for those who don't know). According to most reliable sources, all phaser strips are arrays of individual emitters, each with its own capacitor, and each able to fire on its own. Although the TNG technical manual doesn't fall into the ST cannon, I shall note here that it mentions 200 emitters for the Galaxy 'main array', which I think may refer to either or both saucer arrays. It's not entirely clear to me why they channel their power into a single beam rather than firing all of the emitters at once, but clearly that is what we see. So, technically, what you want is at least several turrets per strip, which, when one fires, causes any others firing on the same ship (subsystem?) to fire invisibly, and with no visible damage or shield effects. There are some variations on how you could do this, but I'm no FS modder, so I don't know what the best way would be.
Either way, you want only one shot per ship, and you want damage to be accounted for properly. As to preventing a ship from firing on too many targets at once, that would probably require some sort of AI script telling ships to concentrate many beams on large ships and shoot individual beams at fighters. The rest is taken care of by a good beam cooldown value.
