The council from Avengers & Winter Soldier is the World Security Council, to which S.H.I.E.L.D. answered -- remember, they sent the nuclear weapon in Avengers over Fury's objections? "I recognize that the Council has made a decision, but given that it's a stupid-ass decision, I've elected to ignore it."
Given that Fitz was the one to figure out how Skye had changed, I think Coulson made a mistake only asking Simmons to help on the gauntlets. I know he is the champion of "different, not bad!" (understandably) but he knows the danger Skye herself faces without controlling her powers, much less the rest of the base. And world. Shutting him out of an engineering project, and one to help Skye, isn't going to end well.
Ward is so psychotic. You can tell because he's calm.