When I was doing this quest I determined that both Tenpenny and Roy were no better or worse than each other, and like you, that the people of Tenpenny had performed no transgressions worthy of death. The solution? I killed both Tenpenny and Roy before any of the other events could transpire, which IMO equalizes the situation about as much as one can within the framework of the game. Roy was obviously no better than Tenpenny regardless of his current physical state as a ghoul. Snobbery isn't a death sentence, nor is bigotry as detestable as it is.