It's a complete steaming pile of bullcrap we've come to expect from this incompetent bunch. I cannot believe for one millisecond that this was so highly classified that even the president was kept out of the loop.
You’re misinterpeting a lot of things here. Nobody said anything about the FAA “clearing military flights for air worthiness”. The FAA absolutely needs to be told and was told about these flights because the FAA is in charge of managing the incredibly crowded airspace around NYC, but they were probably not clear on just how close to buildings the planes would be flying.
And nobody said anything about President Obama being “kept out of the loop” for any reason, and certainly not because the flight was “so highly classified”. You can be sure that President Bush (or possibly Clinton, whoever was President at the time) had no clue about the details or timing of the AF1 flight that took the pictures of AF1 flying over Mount Rushmore — the picture that the new Statute of Liberty picture was intended to replace. In the normal course of events, publicity photos of Presidential hardware is trivia that the President doesn’t need or want to know about, so of course he wouldn’t have known about this one, other than perhaps to have approved the general idea of a photo of AF1 with the Stature of Liberty in the background to replace the Mount Rushmore photo (which was some sort of official publicity photo of AF1).
If some White House PR dude suggests to the President that the AF1-Rushmore photo be replaced with an AF1-Statue of Liberty, the normal repsonse from any President would be “Yeah, sure Joe, that sounds like a nice idea, go ahead and do it.” The President is not going to assume that the US Air Force requires supervision to accomplish this task — he probably wouldn’t even trouble himself to consider whether the photo would be shot directly or Photoshopped, much less how close to the Statue of Liberty the plane might fly if the photo was taken directly. It’s not his job. He has discovered the hard way, that one or more people in charge of things like military flights and AF1 are nowhere near as competent as he might have assumed (and remember, there’s no evidence that anyone directly involved with executing this “mission” is an Obama appointee — senior military personnel don’t change with administrations, and President Obama has even retained President Bush’s Secretary of Defense). Louis Caldera presumably made the same assumptions when he approved the photo-taking flights — again, he was almost certainly approving it in a very general way, reasonably assuming that the people who’ve been operating AF1 and fighter jets for many years, would continue to do so in a sane and rational manner.
What’s pretty clear is that there were communication failures at various levels, including within the NYC government. The people in Mayor Blooomberg’s administration who got the notification and didn’t bother to mention it to the Mayor, assumed that the flights were to be carried out in a way that wouldn’t cause any public alarm beyond a handful of people calling 911 for reassurance when they saw a jumbo jet being tailed by a fighter jet somewhere off in the distance. They very reasonably didn’t imagine that the planned flights were going to go unreasonably close to buildings in a way that was guaranteed to cause mass panic — they assumed the US military knows what the he!! it’s doing and wouldn’t do something colossally stupid. Somewhere up in the military, presumably somebody had planned the flight in detail, but then somewhere between that person and the person directly notifying the FAA, local governments, etc, there was a miscommunication about the specifics of the flight and thus about the need to either suubstantially modify it or do a large-scale advance public announcement about it. Again, there’s no evidence that any Obama appointees were involved in this chain of miscommunication. We won’t help avert future incidents like this, by pointing fingers at the wrong people.