Technically speaking - this problem affects almost all the races in the Star Trek mod:
For example, consider the Romulan Warbird at nearly twice the length (
) of a Galaxy Class starship...yet it seems to be at the same level (or maybe even less) in terms of combat.
Using a few custom mounts for some ships easily fixes any size issues. It's fairly rare that smaller ships outgun larger ships so it's not like dozens of mounts would be needed, just a few for some ships in each race. Heck, you could even make it for a specific weapon on a specific ship if you wanted.
Of course, you can also change the kT sizes since they are fairly arbitrary to begin with - but how will some feel about a "600kT" Defiant and perhaps a 500kT Nebula Class? This is usually why I mention specialized mounts every time this issue comes up. It keeps the canon junkies tamed...
Ultimately - any Star Trek mod for Space Empires can't be exactly the same as the show. That would just suck the fun out of any mod because it wouldn't be balanced and all the emphasis would be on the Federation etc, etc.