The 'honest cop-rule' stops when your own life or the family is in danger. It is said Gaspipe Casso the former Lucchese underboss killed an undercover agent who infiltrated his crew in the 80's. If the Bonnanos knew Brasco was an undercover-agent he would have been killed without a doubt. But I don't know in what way or by who. Because it's quite delicate to kill someone who is closely monitored.
It also depends who found out Brasco was an agent.

If only the members of the crew that Brasco infiltrated would have found out he was in the FBI, would they kill him without telling the rest of the family, fearing for there own lives (for bringing him into the family)?