Well, if you remember when you first encounter them in Nipton, the reason they gave was that "they were a town of liars, cheaters, and thieves. The mayor sold out his own people."
i dont think putting them on crosses, burning them alive, and letting only two live to spread the word is morally sound at all.
when you first get there, the dude with the wolf hood asks you to go tell the NCR what they did, which leads me to believe that their attack was less to do with finding Nipton despicable and more to do with terrorizing the NCR.