If the PWM is the base signal used to drive the motor I doubt you will have any problems. One of the advantages of using the microcontroller should be the ability to add a feedback loop too, that would definitely solve any drift problems. But I assume that the PWM is not being used as a timing signal, just the drive signal so it shouldn't be a problem.
Ahhh, I thought you were controlling the speed of the moter by driving it with a PWM signal, the 50 Hz being the basic signal that is used. What is wrong with using say a 1000 Hz PWM and just adjusting the duty cycle as a function of number of pulse counts? It sounds like it should be the same as what you are currently doing but the rise and fall of the pulse will have tighter restrictions on it than a slower 50 Hz pulse.
