Microwave safety after repainting

Too generic...Did you use the high-temp appliance enamel recommended, or a spray...or worse?

Was the rust inside where it can contact food through the circulating air, or on the outer body?

First thought based on how I read the question: Never use that machine again...but that's based on the word "in" instead of "on my microwave".

If the rust was around the door frame, outside the seals, and you used an enamel (of course) then you may be OK...but...
Considering the fact that a cheap microwave is a drop in the bucket when compared to your family's health...Why risk it?

It should be OK. If there was rust around the door seal, it should be checked for leakage however. I would NOT use black paint internally as it might have carbon black which dissipates energy.