In every case where the .gov flips a felon, it's always because they want a bigger fish or they are trading one 10 pound fish for 20 one pound fishes. At that time, there was no bigger fish than Gotti. Gotti had embarrassed the .gov so much that they wanted to nail him to the cross at all costs including letting the 2nd biggest fish walk after minimal time for 19 murders. One could argue that Sammy was more of a criminal than JG but the .gov still wanted JG more because of the public's perception of him.