not sure this is possible on the ISRs short of physically severing the circuits to the device. (please do not do that!)
also, no information on cco about disabling this device on ISRs. NONE!
there is some reference to interface numbering as USB 0 or USB 1 but i cannot get to this as an interface or find any 'disable' option in any documentation.
see this link for more info:
http://www.cisco.com/en/US/products/ps5854/products_installation_guide_chapter09186a00802c5af1.html#wp1093972