Did they call the bomb squad and evacuate the school? If not, then it would seem they didn't really think it was a bomb. If they did, then wow that is terrible journalism by the author of the article.
The initial overreaction is vaguely understandable*. Especially when you take the Iriving Texas and kid with Mohamed in his name parts. The follow on is not.
He was suspended after they knew it wasn't a bomb. He is being threatened with being charged with making a hoax bomb after they clearly knew it wasn't a bomb (given the proposed charge).
* That it is, is a good indicator that the US is screwed of course, and apparently succeeding in its attempt to destroy creativity and so on. Holy crap the things we did at school less than 4 decades ago - we'd all be serving lifetime prison terms these days.