He didn't go on the lam after Bruno's shooting, he went on the lam after he was indicted for perjury for lying about his involvement in the Bruno murder, claiming he had no involvement at all. And he was allowed to live because he was protected by The Gambino's. Carlo & Castellano themselves, supported John Stanfa, as well as John Gotti. He had a familial tie to Carlo, that dated back to their origins in Sicily. When he was on the lam, he was driving a car which was leased by a Gambino soldier, they funded him during this time.

And the details of Stanfa being Bruno's driver & present in NY when Caponigro & Salerno were killed, didn't become public until much later. There's no telling who knew what within the Philly Mob. But Stanfa was believed to be a suspect by law enforcement from day one. Again, the timing, him being in federal prison for much of Scarfo's reign on the perjury rap, and his connection with the Gambinos is what kept Stanfa alive.