Here's what John says about the song on his web site:
I am not a journalist, I am a songwriter and in the spirit and tradition of the minstrel, I am telling a story in this song.
The story is not strictly speaking, about the town of Jena or this specific incident but of racism in America.
Sounds like Jena Mayor Murray R. McMillin is more upset about this video than he is about the idea of nooses in a "white" tree. 73rd virgin has the whole story over at Docudharma. Check it out.