At first I wanted to say, "If he were white today the same thing would have happened," but the more I imagine a nerdy white kid with circuit board in a case, the more I think that race played a big role.
Cover-your-ass security theater entirely incentivizes responding to every possible issue with the most drastic possible response. There is no incentive to worry about the side-effects of putting a 14 year old on the "no fly list". Instead, they're all trying as hard as possible to make sure that they're not the person that okayed somebody bringing a bomb to the science fair.
Of course everything they've done after the science teacher cleared things up has been incredibly wrong...
I live in a very, very conservative area, where minorities are given a lot of crap.
If I had brought to school what Ahmed did, I probably would have been dropped with two to the chest and one in the head by the school cop and then double-tapped on the ground. Maybe I just would have been tased, handcuffed, arrested, and recommended for expulsion as per the school district's zero tolerance policy, but since I had long hair and wore lots of black clothing at the time my school probably regarded me as the most likely Columbine copycat candidate and would have reacted appropriately.
Ironically, this was in an affluent area with plenty of wealthy foreigners living in the US. There were a few Muslim students at my school, and aside from juvenile idiots I'm sure there was almost no islamophobia, and certainly none on the institutional level. But everyone has stereotypes they fear, and if you fall into that as a child in the school system god help you.