Have him change it. There was a reason you wanted the lights centered over the island, so don't try to talk yourself out of that reason just because the worker goofed. Yes, it's a pain but you'll probably curse the poor innocent pendants every time you walk in if you don't.

Thanks barncatz! We went by there this morning and spoke with the cabinet installers. Instead of moving the lighting they're going to scoot the cabinets up about 5 inches towards the pantry so the pendants will be more in the center of the island top. There's more than enough empty space on that side to move the cabinets over and it will give us a little more room on the side for the overhang with stools under it.