It should be noted that the word "murder" is generally used in two different ways. One in a legal sense, and one in a moral one. I don't think you'd see many people stop referring to the Nazi killing of Jews in the Holocaust as murder, even if it was shown that what the Nazis did was completely legal. On the other hand, Carl Lee's killing of the men who raped his daughter in "A Time to Kill" was clearly murder, or at least manslaughter, from a legal standpoint. But many people (including me) would not consider Lee a murderer, because they would see his actions as morally justified.
While almost all of the killings the Corleones did were legally murder (perhaps Vincent's shooting of the men who broke into his apartment in Part III was an exception), I have a hard time seeing most of them (at least in the movies--I haven't read the book) as murder in a moral sense, since they were killings of other underworld people or their associates for reasons the "victims" themselves would have considered legitimate. For example, not only was Moe Greene a gangster himself, but there's very little doubt he would have killed Michael had their positions been reversed.
That's a good point too IMO. The majority of murders that the Mafia did, at least in the context of the films, were for "business" reasons and were to people involved in and associated with the "business". They weren't just random killings because some guy looked at you funny or called your wife a whore.
I think that Vito might have decided to kill the two guys if Bonasera was a known associate and the beating of his daughter was done by, say, Tattaglia thugs. In that case, the victims would be involved in the business and doing the act for business-related reasons.
Since they were just punk kids, and Bonasera wasn't involved or associated with the business (in fact remember he's in the doghouse because he rebuked Don Corleone's friendship!) and the beating of his daughter was a "civilian" matter, murder isn't on the table because "That is not justice. [His] daughter [is] still alive"
