How to disable Due USB power?
Disabling USB power is slightly tricky, as the incoming USB power is not only used for potentially powering the system, but it is also used by the various USB interfaces to indicate the presence of a connection.

The best way, looking at the schematics of the Due, would be to remove one or both MOSFETs that switch the USB power - that's T1 for the native port and T2 for the ATMega interface.  That will isolate the USB power from the 5V system while keeping it connected to the VBUS pins of the relevant microcontrollers.