You can't really be serious that it isn't a security issue. It should be quite obvious why you wouldn't be blatantly advertising this photo op publicly. I highly doubt that the AF/government didn't expect some sort of stink would be raised by the public who witnessed the fly-by, but that potential for a small public outcry was justifiably decided not a large enough factor to outweigh the issue of maintaining a secure environment in which to operate this special aircraft.

I expect that the 'concerned' public will have forgotten all about it very quickly.