When your threat model is two guys with a pickup truck and an angle grinder your only real mitigation is a claim against your insurance policy.
I think market is very close to a solution. I'm waiting for shipment on a Boomerang, which is an anti theft GPS that secures to the frame's water bottle attachment points. It's designed enough around connectivity that I could imagine motor lockdown in the next iteration.
Unfortunately one of the most competent motor builders, Bafang, just moved to a more closed CANBUS interface to penetrate markets that heavily regulate speed. Bosch has anti theft logic in their systems but there seems to be a smaller ecosystem for modding.