The single-pulse damage for the LRed isn't that high.
Well, sure, if you compare it to the BFRed & LRGreen/BFGreen, it's not that overwhelming per pulse, roughly on par with other destroyer-grade beams, meaning that they kill most big things in 4 or 5 shots.
Anyway, in the past, I've had battles that involved special hit points, to increase the overall durability of particular ships, beam-resistant armor to make player bombs more impactful in comparison
(and prevent destroyers from lol-stomping ships in less than 40 seconds), as well as beam-locking/fire-beaming as needed.
Overall, when balancing a significant battle, I'd say trimming it down - reducing wing-size, make a fighter or two stronger, playing with AI ranks, etc. works better than "escalating" it (adding more ships or wings). It then becomes easier to have player actions have impact, and makes it easier to micro-manage the various parts of the mission.