Is there a way to programatically turning off the power or killing a USB port on the Mac?
I believe that the USB power typically comes directly from the power supply. It might go through the motherboard or some other hardware to combine it with the data lines, but I don't think the voltage ever goes through any programmable circuitry. If you wanted to deactivate the data transfer, that would probably be possible since that is handled by an extension file (IOUSBMassStorageClass.kext), but short of modifying the port physically, I don't think you will be able to deactivate the power.
If you're refering to USB storage devices, according to the Tiger Security Configuartion Manual (pdf):
6 To remove support for mass storage devices (e.g. USB flash drives, external USB hard drives, external FireWire Hard Drives), drag the following files to the Trash:
IOUSBMassStorageClass.kext
IOFireWireSerialBusProtocolTransport.kext
7 Open the /System/Library folder.
8 Drag the following files to the Trash: Extensions.kextcache Extensions.mkext
9 Choose Finder > Secure Empty Trash to delete the file.
10 Restart the system.
I've seen some other stuff around but it's all much harrier. Leading gluing the ports up to get suggested quite a bit.