First, please, please, reassure me that you are not thinking of this for the first Arduboy. Sound output on a connector has never been part of the promised capability, and this is definitely not the time in the cycle to consider new functionality.
If you want to output sound, I think whatever solution you propose should output the sound that people are already generating. I think you would be far better off routing the existing audio connections to a new connector.
A: surface mount 3.5mm closed circuit stereo - http://www.switchcraft.com/productsummary.aspx?Parent=529
B: surface mount 2.5mm closed circuit stereo - http://www.switchcraft.com/productsummary.aspx?Parent=21
Although the 3.5 mm jack would be compatible with regular headphones, the 2.5 mm one is only 4mm high. From the reference drawing, it appears to have only plastic and ground exposed on the top, so the 4mm height could be placed inside an "edge cutout" in the top cover, rather than completely covered in clear plastic.
My reading of USB specs in general says "do not do this at all". USB lines are tightly controlled in terms of resistance and capacitance, and adding anything to them that can't be unplugged is likely to cause problems for actual USB connections. You can also never really test this - it may be that this would interfere with an existing USB host that would normally function just fine, but since there are likely thousands of distinct USB solutions out there already that you can never test, this is one of those cases where it really is necessary to design as conservatively as possible.
Secondly, USB lines have voltage protections distinct from regular chip lines. It might very well be the case that even some normal voltages on a USB port could cause problems for pins on the Atmel chip.