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.