Stumbled on this same problem too... I think your best hope for now is to experiment with the
gun's energy consumption and the
ship's recharge rate.
But if you choose to make your mod for multiplayer, then that solution isn't a good choice - if you set the ship's gun energy recharge rate too fast, the client's gun reserves will NEVER empty (i.e. CHEATER!!!

)...
For the server, I'm not sure...
If it's singleplayer-only then I think you'll have it a lot easier on game/mission balance...
Any coder correct me if there's a proper solution, I'd want to hear it too.