Make sure not to cut any of the traces necessary for the CD drive!

Wire the two 3.3v points together. This simulates the CD cover always being closed. The solder point on the top is tiny, so it's a bit of a challenge to get on to, but it's the closest 3.3v point I could find. Wire one side of a tactile switch to the point shown in the picture, and then tie the other side of the switch to ground anywhere on the board.

I tested it and it works like a charm. You don't have the LED indicators anymore, and you don't have the IR sensor (but no one uses that right?). But LEDs are easy to set up on your own. And now you have a square board to fit into smaller cases.