How can I fill and flatten unneeded hinge mortices for painting?
If your doorframes are MDF any patching is going to be visible to some degree. I would try filling it (with slight overfill) with wood putty and sanding it as smooth as you can using finer grit (220) for the finish. It all depends how particular you are - it's very difficult to get a perfect mend on this.
The only other option is replacing that side of the frame which would take considerable time and effort since it's structural to the door. In case you or a future homeowner wants to put a door back in you need to make sure it's attached properly and shimmed.