I do think that she's working with Michael and this is a trap. Otherwise all the weird stuff happening with Dean makes absolutely no sense. Which, granted, wouldn't be impossible with this show, but I'm hoping that's not the case.

Naomi also seemed too forgiving of Castiel's willigness to damn all those 46 billion souls in Heaven so he could save Jack. Her thanking him for inadvertently saving Heaven instead sounded OOC to me; she probably holds grudges, and has zero reason to be indulgent of Castiel.