I agree that the relationship between the transformations and the UN could have been clearer. But then again, perhaps the scariest thought would be if the transformations really were the legitimate signs from an angry God/universe/whatever that they are purported to be in this imagined universe of the story.
I liked the overall story in any case. I particularly enjoyed how we are sort of setup to view Lewis as potentially at least sincere and well intentioned, only to eventually have it hinted that he is less than sincere, and has intentions most modern people would not approve of.
This story reminded me of that old entry in the Borderlands anthology, or at least I think it was in there, where the imagined world is a place where kids are sacrificed to the Fast Food Gods. But while that story felt bluntly over the top and overly didactic in the process, this story felt more carefully devised to mess with the reader's expectations and comfort zones. I can see why it made a Best of compilation - it's topical, challenging and ugly. Does it say much beyond shoving the problem in our face and making us squirm a bit though? I will have to think about that.
The protagonist's reaction to the stoning may not be very moving, but the laughter and sense of everyday business surrounding it and contrasting with his reaction was affecting. I recall hearing of a recent case in real life where a family killed their daughter on some courthouse steps and the crowd there did nothing to stop it. Horror can help us explore the strangeness inside the human spirit.