Yup, as long as that pinion is not rubbing anything, it should be fine. You are still above the mark on the pinion where you can't allow the gear to ride. If you are really worried about this, you can always grind the flat spot on the shaft lower. Just stick the motor in a ziplock bag, poke just the shaft through the plastic, and seal the other end. Grab a file or the dremel and go to town (so to speak). Just make sure to make it flat and even with teh other flat spot.