"Because Jonathan actually likes his job and would rather I not destroy it," Scarecrow said with an easy shrug. "Let loose...I would nto bother to hide who I am or what I am, which makes it rather hard to run Arkham if the entire world is trying to restrain me." he pointed out.
Not to mention, if he was truly let free, Scarecrow would happily let the Beast run free, tearing the City apart with his claws. Jonathan would not be pleased to wake up in tattered clothing, to find blood soaking the streets thanks to him...again.