The three closed institutions are humanitarian institutions. They were closed because of the political affiliation/inclination of their managers. I doubt even that Hamas is an illegal organization in Jerusalem. As evidence: There seem to be no charges against against the Israeli Arab organization (by Sheikh Ra'ad Salah) for sponsoring one of the institutions. Freeddom of association is granted to Israeli Arabs but not to East jerusalemites.
U.S. to defend Syrian rebels with airpower, including from Assad (Reuters)