Hmm this is a touchy subject. I guess it would come down to rank. Since you are role playing a member of the military if you are given an order by an officer of higher rank then you would follow your orders. I would say that maybe an indipendant could not be ranked above a certain level to prevent a player from creating say an Admiral and ordering the official factions around. But as i said if you are RP'ing a member of the military then you would be sworn to follow orders.