Not really. I can believe in an axis of order vs. chaos and an axis of altruism vs. selfishness as a somewhat viable way of looking at life and not believe that means specific species are only worth killing. I fail to see any mandatory link between the two whatsoever.
I wish there was some additional option with the one peaceful troll. He seemed so disappointed. And even the troll boss seemed to imply that they do what they do because they don't have an option.