I'm not about to attempt to justify anything here, but I did want to call attention to the fact that politics and dealing with children's parents is a pretty sticky wicket!
Just as you can no longer joke about bombs in an airport without getting "special attention", schools need to show enough attention to appease parents. It may have been clear fairly quickly that it was not a bomb, but the initial suspicion may have been made public such that the rumors would be flying. The school may have brought in police as a display of due diligence...
or maybe it was a case of bigotry, plain and simple.
I do believe that once the police were involved, they Barney Fifed it. Cops hate a call like this because they know their actions will be scrutinized by the public eye, but they really don't have proper training for it. Generally, the safest thing (from there perspective) is to be overly suspicious/cautious. Depending on their upbringing/culture, their level of paranoia associated with the kid being Muslim is the nasty wildcard.
Now that it has been politicized by the media, I'm not sure we will ever know the truth. The truth will be out there, but so will the spins on the truth and once that happens, there is seldom clarity.