I would say its highly unlikely that you could disable it. I've never seen that option or a use for it. What you could do though, rather than modifying the motherboard is make a short USB lead up, male to female, and then cut its power lines.
I think you can't do that. You can only disable the usb port in the bios for some MB. If you use a hub to expand the usb port then you have the option to use an extra power to the usb port in the hub (in case a device needs more and the power from your computer is insufficient - hdd, etc).