It was my impression that burning the flags was done to elicit an emotional response from the students and they were instructed to write a paper based on their response. This would be followed by classroom discussion about the constitutional protections and the law.
If I'm correct in my take on what was planned, then the teachers mistake was involving himself rather than show a video of someone burning a flag.
I can see the value of getting the students gut reaction on paper first, rather than having them rationalize what the thought they would feel seeing a flag burned.