The system should have the ability to tell the blocks to stop working, even if they have material in the buffer for item management. A couple ideas include a strong redstone signal from a side and/or a manual switch inside the GUI to turn on/off the system; this would allow the system to be used in multiple ways (either feed items in as needed or turn on as needed with an already full system).

This is actually supported already. You can disable machines with a redstone signal.