You should insist that the 'gunsmith' purchase or pay for a replacement model of the gun he destroyed.
As far as what can be done to repair it, I have had two friends that experienced the same exact buggered up, off centered and improperly spaced work on their MKII pistols. Welding the holes and starting over is will look the best but is obviously the most labor intensive, is it stainless or blued, if it is blued it will require hot bluing again and depending on the filler metal used, the dissimilar metals may show in the bluing.
If you want cheap and relatively easy I would consider modifying your existing rail by adding your own new screw hole locations near the originals and re-drilling the receiver to allow mate this new pattern. I would shorten the rail on one end or the other if doing so will still accommodate your intend mounts and sighting device so that the rail can be shifted fore or aft to keep the botched holes from showing through stock rail hole locations.
If were to do this I would source a steel rail section if possible so that the new holes could be parkerized or blued to a perfect match, if you want to use an aluminum rail you can use Aluma Black or some other such product a pretty good result.