I'm with VL on this one. Yes, Cicci broke omerta, but he did so following the example of his own boss. And he did Michael no direct harm. He answered the key question, "Did you ever get a direct order from Michael Corleone? Or was there always a buffer?", he said, "No, I never talked to him." So Michael had reason to give him a pass.
However, there was no Witness Protection Program when that scene was set (ca. 1959-60). Cicci might have gone into "protective custody" in a prison. Or they might have let him walk in return for his testimony. In either case, he'd have been fair game.