That's pretty much what he meant in my view. The mafia murders people, this is true, but in their eyes all murders are generally justified with a reason. Bonasera wants the two guys killed for, in Vito's eyes, petty reasons and not for a legitimate reason; he simply wants vengeance because they beat the shit out of his daughter because she wouldn't put out. To Vito, that's not an acceptable reason to go and have people killed (although as he indicates, had they killed her THEN murder would have been acceptable. An eye for an eye, and all that).