Brasco was "on the record" with Lefty (and not all associates are "on the record" with a made guy). All killings have to be approved by higher ups. It´s not like Mirra at will could go around killing associates, especially not guys who were "on the record" with the Bonannos, without any reprecussions. Anybody who thinks Mirra could do this, need to learn how to differentiate the Mafia from an ordinary street gang.
It was Lefty who officially had claimed Brasco, even though Brasco knew Mirra first. The sitdown was about Brasco secretly cutting up junk money with Rocky, another undercover cop, who was "close to" Mirra. Mirra wanted a portion af Brasco´s share, claiming Brasco belonged to him. The sit down ended in Lefty´s favor because it was determined that Brasco belonged to Lefty. If it would have gone in Mirra´s favor, Brasco would have been in deep shit, to say the least.

I don´t know what happened to Rocky. The guy is a mystory. How exactly he was persuaded by Mirra to go along with his scam is beyond me. Rocky was a cop but in this situation, he took a huge risk by letting himself be the cause of somebody potentially getting killed. (I doubt he knew Brasco was a fellow cop.) Talk about a bad day on the job! What was he thinking??? Somehow though, Mirra must have had his claws deep into him.

The files released on Mirra are heavily redacted. But one need to be blind not to see the very detailed accounts on Mirra´s wherabouts and business dealings from around 1981. Mirra, if an informant, could easily have been the source who provided the FBI with this detailed info. If not an informant, the info probably came from Rocky.