Well it sounds great, for a regular server, to be able to halt the machine even when power is supplied. But for IoT most people, would want to have a device that would boot immediately when power was applied/restored.
In the scenario you describe, the device would need physical interaction to reboot, so why do you require a software solution to shut it down?
If you must kill/start the linkit, then you should consider using another board/microcontroller and a driver circuit using a relay or transistor or both to be able to turn on and turn off the linkit. For the price, ~$15, you could use a second linkit to do the task.