Apple - Software-only way to disconnect and reconnect a USB device?

if you felt bold, you could disable all of usb service and then reenable. I believe that will do it. will also kill keyboard etc.

kextunload IOUSBFamily.kext
kextload /System/Library/Extensions/IOUSBFamily.kext

it will take some more discovery, but i think this might be a good path. let us know if you experiment

all usb extensions in 10.8 at least:

/System/Library/Extensions/IOUSBAttachedSCSI.kext
/System/Library/Extensions/IOUSBFamily.kext
/System/Library/Extensions/IOUSBMassStorageClass.kext