From the quick googling I’ve done, it may be possible to disable/enable raspberry pi usb power with commands:
Disable
echo 0x0 > /sys/devices/platform/bcm2708_usb/buspower
Enable
echo 0x1 > /sys/devices/platform/bcm2708_usb/buspower
However I haven’t tested. I’d recommend writing a new module that handles this and listens for the USER_PRESENCE event notification that the Pir module triggers.