You're right, but I don't think that would have to be the case. I'm guessing they'd probably pick a time right when the first set of planes was to be over a city, and make that 'go time' for all parties. It would be safest for them, and more terrifying for us. Some planes would be over cities, some over land, some over water. We'd have the full range of crash site dramas unfolding; desperate searches at sea, urban sites with chunks of airliner spread around, rural hills with emergency vehicles swarming around. A true disaster.
All true, it would be total chaos for a while. But as you know, this would never happen, it's just a conspiracy to keep us scared and take away our freedom (that last part is sarcasm).