Brainiac at the Boston Globe has a post on the history of the phrase "Teach the Controversy." It is also a plug for the Amorphia t-shirts, which are priceless. He states that, innocently enough:
The phrase was originally coined by Gerald Graff, a (liberal, secularist) professor of English and education at the University of Illinois at Chicago. Graff wanted teachers to remember that taken-for-granted knowledge is not simply given; knowledge is created in a crucible of debate and controversy, he argued, and it's healthy for students to understand that.
The phrase was then co-opted by Philip Johnson of the DI, who turned it into the action cry of the Intelligent Design Movement, manufacturing a controversy out of whole cloth. Sadly, at the tail of end of the article, he reprints a letter from someone who didn't get the joke.