I have used your idea of putting a backing plate behind the hole I want to enlarge. It works pretty well. I would start the hold from the side you want to protect. After getting the drill bit started and through the backing plate run the hold saw in reverse until you get through the gel coat. This should keep the gel coat from chipping.
The other option (if you don't care how clean the hole looks) is to use a RotoZip or Dremel and free hand the hole enlargement. This will create lots of dust so I would tape a box over the hole on the inside of the hull to catch most of it.