IIRC, there is a way to use EOS Utility for copying the firmware image to the camera. It should be described on Canon's firmware download page.
If that doesn't work, try using a CF card reader for copying the firmware file to the card. The camera itself doesn't support mass storage protocol, meaning that the USB connection can only be used to transfer image files (PTP protocol).
The contents of the card have no permission management since the cards are formatted with FAT32.