Frankie was an exceptionally sympatico character--a small-timer caught between two titans, Michael and Roth. And he was a victim in more ways than one. Michael roughly threw aside Frankie's loyalty to him by favoring the Rosatos and Roth, because he was greedy for Roth's Havana deal. And, Michael cruelly manipulated Frankie into meeting with the Rosatos--in effect, putting Frankie's head in the lion's mouth--so he could either get rid of a vexing problem (if frankie settled with them); or, if killed, further proof that Roth was behind the Tahoe attack.

BUT:
Frankie broke omerta by agreeing to testify against Michael. He couldn't be given a pass. The nominal reason is that Michael had to make an example--no one can betray him and live. And, although Frankie's credibility as a witness against Michael was shattered by his renunciation of his affidavit, the Feds weren't going to keep him on the government's tit forever. They'd keep hammering him for more and more information about Michael. Sonner or later, they'd get something that they could act on without having to use Frankie as a witness.

BTW: It was too bad Paramount couldn't get Richard Castellano for II. But Michael V. Gazzo was a worthy substitute. IMO, he made II.