That's because Bonanno was on the run and they couldn't get to him. And after years of conflict within the Bonanno family they finally decided to make a deal with him to stop the violence which was bad for business. And Bonanno wasn't just anybody, he was well respected in the underworld for being boss of his family for over 30 years. Bonanno made his bones when Gambino and Lucchese were dating cheerleaders.
IRL two different men get passes from non-relatives even though they were actively involved in murder plots (and in Bonanno's case) came up with the plan and did so twice and yet walked away clean. In fiction a man whose involvement is ambiguous and is related to the boss gets no mercy?
Of course that will engender discussion, which is all good...