MCU Input Protection
Your circuit is way over-designed. Try something simpler, like this plain diode limiter



The 5-ms-like bursts are NOT high-frequency by any means. If you can afford 10k series resistor (R1), the above circuit will serve all your cases. 

If you don't like having +4 V on MCU input, reduce the reference 3.3V voltage to 2.5V rail. Or use Schottky diodes. The capacitor C1, if placed in close proximity to the diodes, will also protect your inputs from any ESD.