In my humble opinion, your only solution is to replace the shingles that have paint on them and just recognize that for awhile they will look obviously different. Over time they will weather and tend to blend in but not totally. I am not aware of any safe technique to remove the paint from the old shingles---did you consider trying pressure washing them --I don't even know if it would work and it might damage them too. Tell the painter he needs to correct it to your satisfaction ....and I would make him pay for replacing them by an experienced roofer. Good luck and let us know what you ended up doing.