A couple of things: first, Tom was an inexperienced consigliere in GF1, and there was a certain measure of bad luck that he was essentially in training when Vito was shot.

With respect to Frankie's survival, I think that it is at least possible that much more information became available at the instant Questadt announced that there was a secret witness. No need to keep the secret after Michael had gone on the record, and it would be natural for people to start to talk to the press or others while the story still had some value.