It's clear to me that Fredo did not have to die. Exile was sufficient to remove any possible threat to Michael. If he were really a threat, Michael would not have waiting until Mama died to have him killed.

Roth would have remained a threat, even though he was seemingly defeated at the time of his killing. He was Michael's primary foe and, in the world they lived in, could not have been left alive.

I think the Pentangeli situation is less clear. Did he actually break omerta? He signed an affidavit attesting to his Don's malfeasance. But he recanted in the hearing and Tom tells Vincenzo that his family's honor is intact.

In either case, Frankie had knowledge that could put Michael away and came really close to turning on him. For Michael to let him live would have been out of character, to say the least.