Re: The Avengers 2! The Official News and Speculation Thread - Upgrade section 5
Pierce/HYDRA probably prevented SHIELD from inferfering with Killian's plans. Fury would have known that Mandarin was a bluff, but played along with it (because of Pierce). As for the President getting captured, I assume Fury told Cap to hang back and let Tony deal with it.
SHIELD probably even knew Stark was alive after being attacked at his Malibu home.