Can you just load it up with guns?
Pretty much all of the ships are loaded with guns, the ones for fighting just have more gun than the others. e.g. a ship this size could probably swat away most small fighters but if a war frigate comes plodding along it'd be screwed.
In other news, I have my doubts about the whole rotating container bays thing. I mean, it is definitely awesome, but that seems like it would be very difficult to implement from a gameplay perspective. Maybe that's just me lacking experience in game development.