I realize this is an old post, but I was going to make a post on this point but then saw the above point, so I am posting my thoughts here.aprilemoney wrote: I always thought it was strange that Tony would forgive Uncle Jr. and allow him to keep earning. HE TRIED TO HAVE TONY KILLED! And after all that drama, he just lets him off the hook. I understand he wanted Jr. to appear as the Boss of New Jersey but...
It seems Tony has two (self serving) goals in mind by letting Junior 1) remain the boss and 2) keep earning. The first aims to keep the heat more on Junior and less on him. Tony already showed in season 1 he preferred this arrangement. Even though we see the FBI move Tony to "Street Boss" on the charts, better for the FBI to be able to to pursue a case against the Boss in name at least than the former Boss.
The second, as Tony states, will allow Junior to pay his lawyers. If Junior can't mount a defense or pay a (sympathetic) lawyer then he is more at the mercy of law enforcement/the courts. We see the FBI trying to press him to cooperate. If Junior can't select his lawyer due to insufficient funds then it risks certain secrets and activities being spread more broadly or to unproven hands than Tony and the mob might like. Worth also considering that lawyers (who have a lot of information, even if under attorney client privilege) like Junior's with their retainer are somewhat 'on the payroll' so it makes sense to keep them in the fold.
Both of these two goals help to prevent Junior flipping and cooperating. Being old school, whether he would or not is another question. But if Tony was to take the boss position off Junior, we have already seen the lengths Junior was willing go to with Tony if he thought he was attempting that (kill him).
So overall, just good business (and good for Tony too).