If you are saying goodbye to a friend and the 'problem' was their acne on the face, and your friend was going for a job interview, then yes, you can say
'may that acne not stop you' from getting the job.
If you mean a different scenario, then you should describe it more.
It would be correct, but it is not really part of everyday spoken language to express hopes, wishes or recommendations with May... in this way. It would be more usual to hear Don't let that problem stop you or I hope that problem doesn't stop you.