Josey, you forgot fact that in Freelancer, space-based game pirates are:
obviously carrying ID's, IFF and ships mostly associated with unlawful activity. They are mostly killed on sight by local authorities unless they can bring them in easily (which happens rarely). Base is not your regular restaurant - while anyone can walk into shop or bar, to access station you need permission. Being it granted beforehand or blanket for entire faction, by letting obvious pirates in you are supporting them - becoming criminal yourself and making your installation illegal - subject to immediate demolish by navy if negotiations fail.