Having the LED control exposed through the firmware completely defeats this.
There's also the scenario where the LED or the connections to it simply fail. If the circuit doesn't account for that, then boom, now your camera can function without the light being on.
Can't think of any other pitfalls, but I'm sure they exist. Personally, I'll just continue using the privacy shutter, as annoying as that is. Too bad it doesn't do anything about the mic input.