How can I disable a specific USB port in my MacBook?
There isn't a switch in OS X to go and disable some of the USB connections. If you could give up USB entirely, I suppose you could get at things at the kernel extension level, but in terms of a graphical interface, there isn't anything like network preference panes where you could pick amongst the devices and disable one but not another.

See https://github.com/RehabMan/OS-X-USB-Inject-All for a decent discussion on some of the recent changes to USB and kext. It's quite technical, but also well documented case how to modify things at a low level. The details of your situation may depend heavily on exactly what hardware and software version that runs.