Some religions are, as we say in business, vertically integrated. For example, the ultimate authority in Roman Catholicism is the Pope, he is their CEO. Other faiths are less bureaucratic and more collegial, they have multiple centers of authority.
This New York Times article about Iran describes one of the problems a theocracy has when the religion running the country isn't vertically integrated. It appears that Iranian Shia Islam has multiple centers of authority. One of the major Iranian Shia authority centers has come out against the legitimacy of the recent elections.
This could be great news for the protesters and bad news for the incumbents. Perhaps the story of the Iranian "soft revolution" isn't dead yet.
