In the movie, it seemed surprising that
Harrison was able to crash a ship into a city without some sort of defense shield or protective system kicking in to protect the city, considering its importance to the Federation. Is it possible that, during his year or more with Section 31, Harrison used his "superior intellect" to embed computer viruses into various defense systems on Earth, so he could knock those defenses out when needed - like Kirk used the prefix code to knock out the Reliant temporarily in Wrath of Khan? Or, could Admiral Marcus have been planning a sort of military coup using the Vengeance, like Admiral Leyton did in Deep Space Nine, to take more aggressive action against the Klingons - and programmed Section 31 (and the Vengeance) to be able to shut down Earth defenses, when needed?? Could explain why that city seemed to be unable to stop the crash, or protect itself ... 
