This approach can work, however increasing the time constant of the leds would make it so slow to the point of being unusable in practice. It can be done via firmware, but also adding a very cheap external circuit which would be impossible to disable via malware.
The idea is that if any pulse sent to the led would lit it for say at least one second, the attacker would be forced to have their malware modulate the led much slower, to the point that transmitting a small file could require way more time than the drone can fly.