You don't need to make cargo bay doors perse. They would be neat, but it's not really a necessity. Having a hole on the side of a ship should work just fine (carrier stops, pilots emerge). Entering formation with the carrier while inside the carrier should keep the ships from banging around too much. Although this depends on the actual "formation" execution code. Can you make the "formation" rally point be located inside the ship? Or would Freelancer freak out if you tried to do formation with a ship while inside it?
Edit: Make the Cruiser's cargo hold be something like 6000. Then create a single indestructible commodity that takes up 6000 units of cargo space. That way you can't destroy it and large transports can't grab it.
