Read more from Slate's coverage of the Iranian election and its aftermath.
This is not the first time clerical opinion has been divided. In a series of lectures on Islamic government given in exile back in 1970, Khomeini outlined his vision of political Shiism. He extended a traditional concept of guardianship and from it built a political model that would place the most qualified theologian—conveniently, himself—as head of state. Many religious figures, including the hugely influential Grand Ayatollah Abul-Qassim Khoei in Iraq, opposed Khomeini's vision, and some theologians continue to question Iran's model of government, including Grand Ayatollah Ali al-Sistani, again from the relative safety of Iraq.
Clerical dissent has played a determinant role in many decisive events in Iran's modern history, not least in the 1953 coup that ousted Prime Minister Mohammad Mossadegh. Ayatollah Abol-Ghasem Kashani, previously a supporter of Mossadegh's, drummed up popular opposition to the prime minister and sought the return of the shah. Iranian popular memory largely blames pernicious Western imperialism for these events, paralleling the official revolutionary historical narrative that demonizes Britain, the United States, and Israel. Both readings deny agency to Iranians as actors able to control their own destiny.
At present, much hope is vested in the abilities of plutocrat ex-President Ayatollah Ali Akbar Hashemi Rafsanjani to break the current deadlock. Rafsanjani is chair of the assembly of experts, a body of 86 clerics constitutionally empowered to dismiss the supreme leader. Rumors are circulating that Rafsanjani is in Qom—home to many of Iran's clerical elite—and is negotiating on behalf of Mousavi. But Rafsanjani is a pragmatist and a self-server: His silence since the election may well reflect a desire to hedge his bets so as to protect his influence and power over whoever remains in control.
The divisions in clerical opinion reflect multiple alternate visions of Islam. Given the absence of a unified hierarchical clergy in Shiism, supporters are free to follow any senior theologian they choose. This ideological plurality is matched by a surprising amount of political openness in revolutionary Iran. Although direct questioning of the Khomeinist system or the supreme leader is generally not tolerated, political debate does exist. Many educated Iranians, including the religious, are also receptive to Western philosophical ideas: Reformist ex-President Khatami has a degree in Western philosophy; and translations of Karl Popper's The Open Society and Its Enemies are widely available in Tehran's many bookstores.
Ahmadinejad has attempted to constrict debate—back in 2005, he spoke of a cultural revolution. His coup d'état represents an attempt to dominate Iran's political system, backed by the force of the Revolutionary Guard. His actions have already attracted widespread clerical opposition from senior religious figures. This opposition may not succeed in the short term, because these clerical opponents are not major political players, despite their senior religious authority, and also because Ahmadinejad seems willing to suppress opposition with violence. Nonetheless, the clerics' vocal opposition has radically undermined the already tenuous legitimacy of a state claiming to be Islamic.