Just an annoying asside- Technically if we're using what we know of real space physics Swift... it isn't that the beam is instantanious across a huge distance, it is that detection of the beam being fired would be instantanious to its impact. Of course if you have FTL travel maybe you have a way to detect a shot is fired before impact and dodge it (assuming you're fighting light-minutes away from eachother).
Ah.. science... don't break it too much :D
Anyway - easier solution seems to be "charge up and refire times" - making this a game of rock paper scissor. Using a huge long charge time cannon on a small ship means several rounds of not being able to fire - plenty of time for some smaller ships to gang up and obliterate you. I am not generally a fan of those kinds of rps mechanics but it would be the easy solution you're looking for.