How about this for ease of use:
If you plot a multi-leg hyperspace route, then you only drop out at the nav beacon on your last stop. On the intermediate stops, you jump out in supercruise as normal, allowing you to fuel scoop or quickly resume your journey.
If you head in-system from one of your stop-offs, nothing stops you, but if you then dock at a station before dropping in at the nav beacon, you receive a fine - small for your ship itself, maybe 800 credits, but an additional 100 per ton of cargo for customs violation.
Thats a very good idea. You could say we drop out in a safe zone at the end of the journey.