I use the following strategy:
I have a toggle latch with a wireless receiver on the input and a wireless transmitter on the output. This is my bore's primary on/off switch, and it resides in my base (not on the bore). Then, I have a portal frame at my base with a receiver matching the toggle latch's transmitter, which turns the portal on, and a button with a transmitter matching the toggle latch's receiver. A second matching portal frame is installed onto the bore frame and has the same pair of transmitter/receiver. Additionally, at the bore, the receiver powers the portal AND goes to my bore control system (in this case a computer). The computer's program pauses operations when it receives that signal, and that same signal opens the portal. And it goes without saying that the entire bore is permanently chunkloaded.
This basically means that I have a button next to each of the portals which can toggle the portal open and closed, and when the portal is open, the bore is off, and vice versa. It's very reliable.