1. The article mentioned cops bursting into classrooms waving guns around so it appears it was during class time. In that case, the kids just sit tight in the room. In the fire drill, the kids have to do something. In this case, they really don't.
Another factor is that, in a fire or duck and cover drill, there is nothing that can be done about the threat by teachers or students. You can't go get the chain and padlock out of your desk and be ready to knock the crap out of the fire when it comes to your room, or play dead and hope the mushroom cloud will go fry somebody else's class.
Also, as Micro pointed out, drills and real emergencies do have different procedures. For example, fire drill during my HS chemistry class: there was a barricade with "smoke" written on it in the hall about ten feet from the door in the direction of the primary evacuation route, so we went to the other exit doors. Now, smoke doesn't politely hold still as a clearly defined vertical wall in a real fire, and would have reached the door long before 25+ students could file out, so we would have simply tossed a desk through the full-height windows of our ground floor classroom and stepped out that way. Not sure how the administration would react if we'd done that during the drill, but I'm guessing the teacher wouldn't have gotten an award for taking the proper - rather than the directed - action to keep his students as safe as possible.
