I think the first thing I would do is to try to break the two pieces apart by tapping a single-edge razor blade between them. It won't be a perfect split, but if you can work a little from each edge you should be able to do it. And if you shave a little into the wood either way, don't sweat it.

Once you have them apart, sand the glued edges fairly smooth and re-glue them

If not, you could just glue some scrap to the top edges, but when you drill the hole, you'll have to drill it that much higher than the hole that is there now (Or drill the hole as is and file it up by whatever amouint the piece is too low)