I like the OP's idea.
I would alter it slightly though: maintain the current sequence of events, where you arrive from Hyperspace into Supercruise at the star, allowing for fuel scooping and rapid transit to onwards systems as we have now; but add a perimeter around the arrival star - only when you cross over this perimeter into the system proper are you then pulled down into the Nav Beacon instance (via a static interdiction device used only by authorities perhaps), in order to facilitate the things in the OP, whilst maintaining the benefits of the current system.
I would alter it slightly though: maintain the current sequence of events, where you arrive from Hyperspace into Supercruise at the star, allowing for fuel scooping and rapid transit to onwards systems as we have now; but add a perimeter around the arrival star - only when you cross over this perimeter into the system proper are you then pulled down into the Nav Beacon instance (via a static interdiction device used only by authorities perhaps), in order to facilitate the things in the OP, whilst maintaining the benefits of the current system.