Let's be more realistic about it than being emotional, security agencies around the world follow a method called 'profiling', and Muslims are in the wrong end of it because of the continuous activities of some Muslims (not a small number though) around the world in the name of Islam. Crying victim or fighting the authorities won't help here, what rest of the Muslims should do is to fight this evil that is breeding within some sections of their own community.
As for the kid, the school was right to inform the authorities, what if the kid was brainwashed by the ISIS on social media? Everyone would have held the scholl authorities responsible if something actually went wrong. However, the treatment should have been more sensible, the school should have confiscated the homemade clock and hand it over to police for examination without making any scene out of it, and requested the police to visit his home in plain clothes after school hours, as checking the kids belongings was also important. It's better to be safe than sorry, but there was no need to shame him publicly.