The freelancer environment is controlled by the player's REP and not by their Discovery ID, until both are brought into line; situations like unauthorised access to Alaska will remain a problem.
One solution for Independent faction members; why not try sending a quick letter PM/ Email to the faction CEO / Commander telling them who you are and what aspect of RP you like to undertake within their faction. Hopefully together you can arrange the RP and with it any authorisation required.