My garbage disposal is busted and my wife wanted to be rid of it anyways. It's hard-wired and, after some trial and error, I found it is on the same circuit as a GFCI above the sink. (Not the same circuit as the dishwasher).
AFAIK I have two options here regarding the GD romex:
1) Use wire nuts, electrical tape, and a blank electrical box to cap the live wires. Probably nail it into the kitchen cabinet. That would allow a future homeowner to wire a new GD if they wanted.
2) Pull the GFCI outlet and see if the GD romex is just extending off the GFCI. If so, remove and pull the romex completely out.
Advice? I'm a relatively novice DIYer, I've capped a few blank boxes but I don't want to make my house's wiring even more funhouse than it is.