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.
SHIELD probably even knew Stark was alive after being attacked at his Malibu home.