Here are the steps I did.. (add your steps where they need to be for your own unique part)
I did the following the determine I could in fact delete any green pad on the stage.,
1.) Opened Eagle
2.) Opened Adafruit library..
3.) Clicked on the "DEVICE" icon
4.) On the right pane/panel I chose (double clicked) the package I wanted to 'edit' (in this case: USB-MINIB-THM-MOLEX)
5.) I disconnected the pins I wanted (all?) (click 'ok' when done)
6.) Click on "PACKAGE" icon... (scroll down to your part name: USB-MINIB-THM-MOLEX)
Edit/delete as you see fit..
if you have already copied this part to a new/custom library.. you can just save after the edits.. be careful of overwriting current part in Adafruit lib.
hope this helps..
take care.