Good point on if they killed Calabrese Jr. it would bring a ton of heat on the outfit. I do believe that in extreme cases the outfit still kill people, Zizzo for example.
I'm not sure how much I believe Jr. had permission from Caruso to flip on his dad because Nick did the most damage with his testimony. I do think that the outfit were probably happy to see Frank Sr go away because all the heat his family caused the outfit.
Nick is do out of jail pretty much any day now or he may have already been released. It's something that we'll never hear about since he is in witness protection.
A good example on how the outfit used to kill people even with all the attention is the guy who put away Cerone, Angelini and Ferriola back in the early 70's. Louis Bombacino was blown up about a year after all the guys he put away got out of jail. Granted back then they didn't have the DNA technology and stuff as they do today.