This thread is a little stale, but I thought I'd interject real quick:
FWIW: One of the solutions we use, is to just add another set of headers to the bottom of the shield. There are a couple of pictures here:
http://www.shapeoko.com/wiki/index.php/ ... lectronicsLots of people like us (makers) have them laying around, so it's a quick and easy fix. Also, seems to work pretty well and I think it looks better with both components parallel to each other, as opposed to the shield sitting at a slight angle due to the interference of the USB jack.
If you wanted to get fancy and make it even more rigid, you could use some spacers then run a bolt through the mounting holes of the shield and the arduino.