Oh yes I definitely agree, the idea was that the players would be of a more clandestine nature, not overtly criminal or hostile to the Imperium.
it's one of the funny things I notice in Rogue Trader the amount that supposedly become pirates or indulge in other unsavoury activities. Seriously if you have something as valuable as a warrant of trade which gives much more freedom than almost any other Imperial citizen has as well as limitless profit making applications why would anyone risk it by taking part in piracy, which any man with a voidship can virtually do.......