Alignment rules, in many cases, justify why a lot of monsters may be wantonly slaughtered without a hit to the ol' conscience. According to those rules, the evil deities who created certain races made those races to serve them and "have strong inborn tendencies that match the nature of their gods." So most orcs, for example, are evil, act accordingly and deserve what's coming to them. As well, alignment is an "essential part" of the nature of fiends. "A devil does not choose to be lawful evil, and it doesn't tend toward lawful evil, but rather it is lawful evil in essence." You cannot separate the two. And, since they're evil and can do nothing other than act the part, I just can't feel bad when they are bludgeoned, pierced, slashed, and magicked into a chunky goo.
Also, the monster's XP and treasure value really takes the edge off any other concerns.