I do have to agree with you on the need for some realism when it comes to depict marines on the decks. However, I think that there is a better method for the gameplay mechanic. Civilian ships would work in much the same way as you describe above, only being able to support a single crew... Military ships would have a dedicated fighting force stationed onboard, possibly consisting of soldiers you load onboard, removing the need to remain stationary, and thusly making a dedicated navy useful, while still making it possible to retain something in the way of a civilian defense.