I have no strong opinion on your question because of something I have personally experienced.
I went to journalism school and worked for a newspaper for five years. This taught me that journalists generally see the world a certain way. They write stories that support that world view.
When the story challenges or directly conflicts with that world view, the editors change it. They "edit" facts out of the story, so you never really get the whole truth. You get the part that illustrates their view of society, the police, authority in general, etc.
At the start of this story, someone decided that it was going to be a story that said, "Innocent school kid builds simple clock for a science project and gets pounced on by insane authorities simply because of his religion." Any facts that didn't line up with that headline got cut.
I think there is more to this. The media has just left out those facts which would make the reaction of the school officials and the police seem more reasonable to all of us -- the things that would make us each say, "Well, if I knew that, I might react the same way they did."
Perhaps the school did overreact. Maybe each of us, in their shoes, would have called the police.
Without all the facts, it is difficult to say, either way.
What I do know is that we don't have all the facts, and won't be getting them anytime soon.