Right, so the green drivers would just keep resetting the red light's timer.

Ah! That's definitely an interesting case and quite possible.

A way to counteract this would be to interconnect the mics to determine the origin of the sound and its flow. Nefarious drivers honking while passing the green light could be ignored, or have the green light cut short (but then you risk penalizing drivers behind them who might not be responsible).

If the gain is minimal, directional microphones are used, and they are mounted close to the road, this effect can be quite easily minimized.