I had the exact same issue with holes in metal.  I cut a 1x2" rectangle when what I really needed was a 1/2" diameter hole, don't ask me how I screwed that up.  Anyways, I took a piece of wood and clamped it underneath the hole and then took some bondo and filled in the spot so that it filled the area plus a little extra.  After it dried I sanded it down, but it turned out that my spreading job wasn't that great and the other side (where the wood was clamped) turned out to have a smoother finish.  So I flipped it over, sanded it smooth and then using the drill press, I made my 1/2" hole right into the new patch.  I haven't had a single problem with the patch being weak.  The key is to making the existing hole kind of rough.  Take a metal file and rough up all the edges, the bondo will stick better that way.  And when you're using the bondo, do it in a WELL ventilated area.  I did it outside and it still stunk horribly.  Good luck!
Scott