Possibly they should introduce a concept of "nuetral ships" that are governed only by moral alignment. They would be "hirable" and for a number of credits by ships of the correct moral alignment. So for instance with the downfall of the Torians to the Drengin it makes sense that they would naturally align themselves to another good civilization. If a civilization is of identical moral alignment to the ship then hiring nuetrals should be cheap to hire.
The cost should be equivilant to half the ships construction cost, or if it is starbase the cost of all the constuctors that have been added, both to construct it and to add all the needed modules to it. Added cargo and people do not count. If a civ is of exactly the same moral alignment as the hiring civ then they can be hired at a fifth of the cost of construction (ie dirt cheap). However nuetrals cannot be hired by and will attack (and may be attacked by) civs of an opposing aligment. Civs of a pure alignment totally ignore nuetrals, they cannot be hired by them and will not attack them.
Minor civs, if not at war should regularly spawn nuetrals as "merceneries", these neutrals have the same alignment of the mother civ and roam the map lookin for employment.
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