Actually, the three lairs in the Underdark make a better example than "an orc."
Let's assume, here, that the PC goes to the drow city before any of the other Underdark cities. S/he is told that Matron Mother Ardulace wants the blood of a kuo-toa prince, the eye of an Elder Orb Beholder, or the blood of an illithid elder-brain, and where to find them. How is this morally different from Edwin's quest to kill Rayic?
Because it's necessary? No, it isn't--the PC can kill Ardulace, seize the eggs, and fight his/her way out of the drow city. The drow have allied with Irenicus, stolen Adalon's eggs, held them hostage, and planned to double-cross her and sacrifice them; the other Underdark denizens have done nothing to you. (Moreover, I'd actually contend that even if you actually needed the Elder Orb's eye, it wouldn't make killing the Elder Orb justifiable--why should the Elder Orb care about your needs?
CHARNAME: I'm justified in killing the Elder Orb because I need its eye.
IRENICUS: Interesting you should say that--I'm justified in killing you because I need your soul. Glad to see you're making no pretense of a moral high ground, here.)
Because they attack you on sight? If you came into my home planning to kill me and cut my eye out, I'd shoot you on sight, too.
The only reason I can see for the distinction, then, is that the Elder Orb looks, physically, a lot creepier than Rayic Gethras to human sensibilities.
And what about those players--most players, I bet--who explore and depopulate not one of the Underdark areas, but three? When you already have the Elder Orb's eye, why is going into the kuo-toa caverns planning to kill and rob all the sapient beings there, because you can, more justifiable than going into the Temple of Talos and killing all the worshipers? Again, kuo-toa are in no way more monstrous than priests of Talos.
I'm really neutral on whether you should make it "not evil" to kill human monsters or make it "evil" to kill nonhuman ones, but I think it's important to be consistent--and Virtue is not consistent as it stands.