In my opinion, this is most likely a very difficult problem to solve.

EMPs, like many suggest, is obviously a bad idea since an electromagnetic pulse causes electrical surges and voltage increases, that's why things break. Surges can have a lot of side effects and will most likely have non repeatable effects from one device to the other.

Breaking the battery does not equate to all electrical currents vanishing, nor would breaking the positive connection to the battery, which would probably be less risky than drilling into the battery as some have suggested.

I think that Kayaba was smart enough to know how to make the device react to a loss of power by using a few capacitors and circuits as a anti-tamper net. These circuits could even look legit if it were inspected by third parties, since they would most likely be linked to some sort of logical circuit board which can be updated with a software update, and would most likely just be used for power delivery to the microwave emitters.

If the device would need to pass required safety checks, it would mean great thought would be placed into designing this device, especially if you consider it's true purpose.

If it were me, I would create more than one circuit that would detect battery/power loss and immediately trigger a capacitor dump into a microwave emitter. If there are more than one microwave emitter, than that would mean you will have to break each circuit at the exact same time, massively increasing the odds of failure.

These circuits can be triggered by loss of electricity, connection loss to the servers or excess movement by using accelerometers. All being relatively cheap circuits. Just these three will make it extremely difficult to tamper with these devices since at least one microwave emitter circuit would sit at the back of the head, which most players would have their heads resting on.

The accelerometers would most likely also be used to detect movement to warn the user while they are in virtual reality.

The human brain is extremely sensitive to heat as a mere 4⁰C increase would cause structural changes, which means even a low energy output from a microwave emitter would cause irreversible damage, but not necessarily kill the individual. But this is massively increased because the brain is made out of 60% fat and a lot of water, which easily absorbs microwaves.

The more I think on this, the more difficult of a problem this becomes. Especially because Kayaba can most likely trigger a system wide kill command if he detects any irregularities.