In regards to Joe Pistone, the only reasoning the FBI ever gave for pulling him was because they were worried that he was going to be ordered to kill somebody to get his button. In fact, he had already been given the contract on somebody, Bruno Indelicato I believe (they had a couple plans to deal with this problem. if Joe found Bruno, the FBI was going to take Bruno into custody and possibly stage a hit). If Pistone were brought into a room and ordered to kill a man, or somehow put in such a situation, that would be a disaster for an already successful operation and I think they feared such a situation. Anyways...that's the only reasoning that was ever given.