I believe that cap ships brings a lovely dimension to the game, but as in the old earth if a war cap ship wonders into some other countries (space region's) borders without requesting a pass it is a act of war. So I like the arrangement where cap ships are limited to their own borders or no-man lands.
Regarding the large factions like the Corcairs: the large houses are in the out-regions of space (like the drug lords of the old earth) and are difficult to control by the proper governments. Furthermore organizations like that gets allot of money for their unsocial deeds like making drugs and slavery so they can be well equipped with expensive weapons. I don't see the Corcairs as a 'terrorist organization'; a terrorist organization cannot have cap ships because they are hidden amongst civilians (or need to infiltrate) and armies / police can easily wipe them out if they are found.
I think having an odd war between factions are good fun.
