If you want to disable the USB ports on your little Pi, just run this bash script:
https://gist.github.com/marcotini/b52f9d5bfdbad6c37ea92fcd8f82c30b
You can do this with a simple commands:
sudo clone https://gist.github.com/marcotini/b52f9d5bfdbad6c37ea92fcd8f82c30b usb.sh sudo chmod 775 usb.sh sudo ./usb.sh