In theory it doesn't make much sense. IAEA is a UN agency and its role not specific to a single country. He reported in the past that Islamic Regime was complying with the deal and he could now report that they are not complying if they do what they are now shouting before microphones.  His job stops there. So why resigning?
My guess is that he got too cozy with Kerry-Zarif family and the U.S. let him know that they know.