I think there should be a way of doing In circuit re-programing with just a serial line.
I own a robostix but I always use my gumstix to reprogram it. But it uses a regular serial connection and a special program (UISP) to reprogram while holding the robostix in reset. Jon Hyland's brother Dave is whom you need to talk to. Most of the robostix code is his stuff. You might beable to catch him on the gumstix mailing list...
But maybe the way of least hassle is to use this http://search.digikey.com/scripts/DkSearch/dksus.dll?Detail?name=ATAVRISP2-ND
And a rig like this http://docswiki.gumstix.com/Robostix_AVRISP_cable
Connected to the 'ISP' headers (bottom edge near the center): http://docswiki.gumstix.com/images/e/e4/Robostix-Top.jpg
And then use AVRStudio to develop with: http://www.atmel.com/dyn/products/tools_card.asp?tool_id=2724
The i2c boot loader is not installed and it wouldn't help you much unless you have some way to send your programs over i2c (which works very well for the gumstix)
As for the actual program interface you will need to write the software on both sides for a serial connection. I would go with some a PC client / Robostix Server kind of arrangement. So you would have the PC send a request for data and the Robostix reply. Another option if you have a relatively small set of things you need to know form the Robostix is to just have it spam the info out as fast as it can and then just receive commands from the PC.
Does any of that help?