The second episode of the 2nd season is supposed to clear that Junior is no longer a threat to Tony at all. it opens with them confronting each other and ends with Tony carrying Junior. the old guy is fading fast and Mikey P was the real threat. he even agrees that Junior just did what he had to do and more important, Tony was convinced by his lawyer in the previous episode that it's good business to let Junior live.

plus he is one of the trademark characters and they couldn't afford to have Tony whack him - the audience must have something to like about Tony - why do you think Chris gets away with so much shit?