It would be 2 extra instructions to disable the pwm and re-enable it. And people would have to make sure they did it right in the code. I think it was to keep the human error out of the critical overcurrent circuit, so there was no way to really mess it up (Fran made the overcurrent circuit a few months ago for me
Fran's Overcurrent Circuit ). Mostly it's there for PI loop tuning safely, so that if I use a bad P or I, it won't fry the mosfets with too high of a current.
The 10k pull down is also for if there is some sort of microcontroller failure, that the direction of failure is to guarantee that PWM output is 0, so it doesn't do anything weird like float if there was some sort of latch up, which could cause a full-on failure state.