As a student who's massively into the Raspberry Pi concept (and who desperately wanted to get his hands on one :'( ) I understand your vantage point here.
Can I suggest that you use a rounded-edge extrusion from the network port to bring the side of the case level with the USB ports, like this?
Your case design, and in particular the updated version, looks absolutely fantastic (in fact, it has a very slight air of Apple about it!), but as you've rightly pointed out on your site, the USB ports stick out, which could leave you brand new RasPi vulnerable to having them damaged.
With relation to this, does the extra ~5mm make that much of a difference to the cost? With the sole purposes of the case being to protect the circuitry and to make it look neater, you could achieve both to a higher degree by finding an aesthetically-pleasing way of hiding those ugly ports.
Also, did you get your hands on one from the first batch?