(Semi uninteresting facts: The Nuremberg trial avoided actions committed by allied forces plus they specifically avoided trying German 'crimes' that were identical to allied 'actions' so as not to draw attention to them.
C16-17 pirates in the New World were more often than not sponsored by a government - often the Dutch to pirate English ships and visa versa. So as well as your enemies cargo and passengers you got a nice little retainer. Thus piracy was used by governments as a weapon of personal and economic terrorism.)
The main point about not pirating in a cap ship on FL is that of crazy playability problems. Perhaps if all capital ships had their cargo reduced to the same space as an average fighter things would be fairer. *shrug* That wouldn't stop terrorist factions from just sitting in a trade lane with a BS and smoking everything that came through.