The commonly accepted motive for Mirra's murder was retaliation for the Pistone infiltration of the Bonannos.When Sonny was whacked,Mirra figured that he was next due to his association with "Brasco",so he laid low until Joe Massino found a way to get to him.
Although Mirra was duped by Pistone,just like Lefty and Sonny,Massino thought that Mirra was in on it from the beginning.
The feeling (incorrectly)was that Mirra was flipped before Pistone came around,and that he agreed to help with the infiltration,and work with the FBI by being Brasco's inside guy.
From what I understand,Mirra was never a rat,except in the imagination of the Bonannos.