To put it in simple terms, Salemme was a Ray JR guy. It was JR Russo and Ferrara (leaders of the renegades) who forced Ray JR out so Paul figured if you eliminate the renegades, Ray JR would step back in when he was released. By this time, the blame for the bugging was coming off Ray JR and they were learning it was Mercurio the rat so Ray had a lot of supporters and allies coming back to his side. Some of that support was just people longing for the old days of Ray SR and wanting to end the turbulence.

Personally, I think Ray JR was done with the life. He was probably relieved to get out alive. He went on to be 10x more successful in the legit world than he ever was in the underworld. He was not like his father and I mean that in a good way.