Iranian society is rebelling against traditional religious authority in a way which is pretty unprecedented. The question is not whether or not this protestation will have any long-term effect. Best-case scenario is that Ahmedinejad ascends to power as a very weak president. This will have implications on his ability to be influenced by both Ayatollah Khameni and the west. Compared to the Ayatollah, Ahmedinejad has been fairly quiet about election results. It is in his interest to make this dispute about the Ayatollah and not about him. This whole conflict could in fact strenghthen Ahmedinejad, if he can shift focus off himself and into the Ayatollah.
On the flip side of this is the chance of some kind of coup or reform. If this were to happen, it would require two currently non-existent things. The first is a strong leader. Moussavi has been taking an increasingly strong position and has risen to the call of his constituents. However, his ability to speak for the movement remains unattained, and so far dissent in Iran is a popular uprising rather than an organized movement. It is still possible Moussavi could gain leadership status, but he still has a ways to go. The second necessary componant is a series of bad decisions by the Ayatollah and ruling class. Already the Ayatollah has reversed his position about the legitimacy of the elections, a mistake which makes him look indecisive and inconsistent. He has also attempted to quash the protests using military force, the absolute worst method to stop a popular movement. The use of force created a martyr out of Neda Agha Soltan. If bad decisions continue from the senior Iranian leadership, it could fuel protests by making the movement about the decades of veto power the Ayatollah and religious clerics have had over the Iranian democratic process. Instead of the current core constituency of Moussavi supporters, bad decisions by the Ayatollah could expand the protesters core constituency to those who do not support the rule of the Ayatollah and the religious para-government. This constituency is considerably larger in Iran.
Moussavi's ability to step into the shoes of a populist leader, and the Ayatollah's choice of method to quell dissent are the two critical variables to watch in the next few weeks. Even if Ahmedinejad is successfully inaugurated, tension within Iran is likely to continue for some time.
1) "Moussavi Addresses Throngs Who March in Silent Protest in Tehran," CNN, June 18, 2009.
2) "Iranian Woman Killed During Protests Loved Music, Not Politics," CBC News, June 23, 2009.