You didn't say how big the boat was, or if the repaired holes are close to the new motor layout. On my aluminum boat I replaced the plywood transom board, so while it was out, I had the holes welded closed. Welding wouldn't be a option if you have plywood behind the aluminum.
A friend of mine patched the holes in his transom by using a stainless steel carriage bolt and rubber washer. He bolted all the way through the transom. Of course the holes were above the waterline. It didn't look to bad, but everyone would ask why the bolts were there.