I've tried this trick once or twice and it seemed to work:
-duct tape off the larger ko you don't want to remove around the sides
-with a very sharp bit, drill a pilot hole in the center of the ko you want to remove
-then using a hole saw, gently drill out the size you want
the thing is not to force it.
I really prefer cabinets w/o ko's if I can get 'em. When I did industrial I would specify them. It makes it so much easier when laying out your cabinet, and I think it looks a whole lot better too!
-Good Luck!