This is a simple case for USB power blocker for 3D printers, OctoPrint,  or Raspberry Pi. 

Found here: https://www.tindie.com/products/fatmannmakes/usb-power-blocker-inhibitor/

The alignment pins are very small, but I never had an issue printing them.  Put a few drops of CA glue on the corners to seal.  

Optionally  can use some hot glue on both sides of the board.