How do I condition a really noisy pulse for a 3.3V microcontroller
Zener clamp will probably work as you expect.  (Another way of achieving a similar result is to clamp with a Schottky diode between signal and +3.3V supply rail.)
100μF seems too large for a smoothing capacitor.  Together with 6.7k, the 100μF will give you an RC time constant of 2.1sec.  That's too slow for a fast pulse, which lasts less than 1ms.  Somewhere between 0.01μF and 0.1μF might work better.
Do you have a bleed resistor in parallel with the smoothing cap?  Otherwise, it will not discharge between the pulses, and output will remain high all the time.  


P.S.  It's nice that you've labeled the purposes of your components.   But designate the components in the schematic too:  R1, D1, D2, C1.  In the comments, it's easier to say "D1" and C1 than "direction diode" and "smoothing capacitor".