Sure Frankie violated Omerta. Even without an indictment of Michael, Frankie's affidavit would have given the government information they could use to continue investigating the Corleones.

With respect to giving Frankie a pass, I always remember a line from the book that is thought by Kay: "Michael was always fair." Michael, always fair but a crazy *&@%!#$*, couldn't kill his brother unless he killed all his other "enemies," too. And he was going to kill his brother....