I think one of the bits that stood out was the fact that a Gallentean capsuleer was detained by Federation Customs...perhaps legal immunity isn't all-encompassing.
It seemed to me that it was heavily implied that the capsuleer in question (Arete) was known to be working with or for the Serpentis. That would be more than enough reason for Customs to want to have a 'chat' with her, if she was getting off of her ship, and likely more than sufficient grounds to actually do so.
Sadly we have yet to see this kind of realistic reaction to any Angel, gurista, Snake or Blooder pilot in the game, let alone Sansha loyalists.
If the consequences to becoming to involved with the outlawed factions or just hitting outlaw yourself was a warning when you docked saying 'you will be arrested/detained/fined, do you really wish to do this' as you are an outlaw in any 'empire' station, and the only option then being outlawed faction stations hidden around low-sec maybe even some outposts in high-sec, then things would be far more interesting for pirates and pirate hunters alike.
Having said that, I've yet to read this story, and I should and I will, given time, instead of starting some debate over piracy or how easy/biased it is etc. Another time and place for that.