First, FIRE your painter. There is no excuse for having overspray on the roof, unless your painter didn't bother with the hassle of laying tarps down like every qualified painter should.
Beyond that, you have a couple of options.
Depending on how much overspray there is, you can hire a roof cleaner to pressure wash the overspray (and the rest of the molds and crap on your roof) which will minimize the effect. I would recommend this step in any case; it will make it easier to see what you are really up against.
Once the roof is DRY, you can try purchasing a can or two of spray paint tinted to closely match the prevailing color of the roof. The point here is to MIST the roof, don't be piling on the spray, or you will see it, even if its the same color. All you want to do is reduce the obvious "color" on the roof by overspraying the correct color.