I liked this story when I first read it in Asimov's and I enjoyed it even more hearing it out loud. To me the real takeaways from this story are about personal accountability, the grave risks inherent in invoking "faith" prematurely in a given situation, and a nagging feeling that many years from now others will be writing about us and scratching their heads in wonder at many of the bizarre things we do right now in our culture in the name of tradition and blind faith in concepts that are statistically provably wrong.
In this story's world, the new ruler brought his victims to be flayed, and he asked Njeri to clarify/confirm what happens. She could have said that all she knows is that everyone she flays open has some black stuff in them, but she does not know what that black stuff is, what it means, or whether it is inside everyone or not. Instead, she gave her stamp of legitimacy to the practice and he ordered the next victims flayed. As she came to realize, simply following orders does not absolve someone from the responsibility of their actions.
As for the entire practice of flaying people to expose their evil, the sheer stupidity of their reasoning was obvious: Everyone they flayed had black stuff inside them, and therefore they must all be evil. Even though there was no scientific reasoning behind it.
I can't help but think there right now in our society there are billions of people who do, say, and believe all sorts of crazy practices and beliefs that are hateful and harmful to other people -- and they do those things because they believe that they are right or true -- even though they have never sought out proof of their validity. Rather, they falsely assume that because someone they love or respect seems to believe the same thing, they should go along. And the next thing you know we have entire cultures locked in groupthink that leads to intolerance, hate, and war.
I'm speaking partly (but entirely) of religion here, and, while not meaning to offend anyone who is a deep believer, would like to suggest that many religious groups' core beliefs are mutually exclusive with each other. Regardless of what the objective truth turns out to be, if we ever learn it, billions of people are likely wrong about religion right now. Very very wrong. Yet they persist in their beliefs and claim they believe what they do because they have faith in their particular sect's beliefs.
What they should be doing, in my humble opinion, is asking themselves whether they were that lucky to actually be born into the "right" faith? Furthermore, they should ask themselves if they were born into a "wrong" faith, do they think they would they cling to that faith just as steadfastly, or would they somehow "know" that they need to search for the right one?
In the end, our situation and the situation of the stone wall seems to come down to the same thing. A lack of critical thinking, understanding of statistics, and a great deal of moral laziness.
All that said, I agree that the story itself wasn't great for many of the reasons you all pointed out. But I did like how it made me think, and I also acknowledge that I really didn't think these things the first time I read the story because I was rather fixated on the graphic descriptions of the flaying.