People had to build this system. Many people. People had to operate this system. Many people. People had to keep this system a secret. Many people.
Just wanted to point out that the term is really "a few bad apples spoils the barrel"
So a "few bad apples" in this case applies, and those apples are probably the executives in charge of the program. All the people involved who may not normally do morally questionable things, were "spoiled" because of the bad apples.