I believe Tony's intention at the time of finding out the attempted hit was Junior, was to kill his uncle. Tony was so full of rage on first thought that he even said to Carmela that he would "take care of" Junior and Mikey P and get satisfaction. But as you know the FBI indicted Junior and several other Family members at--for Junior--a very convenient time. And as time passed, with Junior under house arrest, Tony realised that with the old man alive the heat was taken off the de facto Boss.

Mick