In the novel, Michael didn't have to kill Cuneo and Stracci because they weren't a threat to him, and he may have been trying to prove a point: that he was a "just" Don, a "man of honor" because he wreaked vengeance only on those who harmed his family. And he made a more subtle point: by killing Barzini, he was showing Stracci and Cuneo that he knew who was behind Tattaglia, even if they didn't. Moral: don't f**k around with Michael Corleone.
In the movie, killing them off made a much more dramatic climax. And if he hadn't knocked them off, what would the Senator have asked him in GFII: "Were you responsible for the murders of the Two Families in 1950 [ sic ]?"