[chrisdalke]

It's probably the wrong place in the stack to implement this, these are very low-cost commodity microcontrollers running the firmware and the design of flight controller software is focused on time guarantees and reliability.

With the exception of low-cost consumer drones, most larger drones have at least a "Flight Controller" (embedded MCU handling guidance, navigation, and control) and a "Flight Computer" (Higher level *nix based computer running autonomy software), and the flight computer is IMO a more appropriate place to put this.

You could encrypt any Mavlink or proprietary protocol at the application layer if you're using an IP link, or you could also just rely on the telemetry radio to perform encryption between the drone and your ground station.