[ThrustVectoring]

Unlikely to be legal - you aren't authorized to delete software in use on company computers (regardless of whether management currently knows it is in use), and the software you wrote is likely a "work for hire" done during work hours in the course of your duties (again, regardless of whether management currently knows about the software and how it gets used by front-line workers).

The correct way to handle this is to get ahold of the CTO or a relevant subordinate in their department, and inform them of the shadow-IT situation going on at the warehouse. Most risk-adverse IT executives would have a conniption at the idea that work policies are enacted by business logic code that zero employees understand and can modify.