Abbas Milani in The New Republic:
The IRGC has largely accepted the leadership of the clergy and Khamenei's role as commander in chief. But while Khomeini strictly kept them out of politics, Khamenei has encouraged them to get involved in his political battles. In his eight-year tug-of-war with the reformist movement led by Khatami, Khamenei used the IRGC more than once to suppress Iran's rapidly developing civil society and student movement. The most egregious example of this militarization of politics came in the 2005 presidential election, when Khamenei, worried about a possible Rafsanjani victory, reportedly ordered IRGC members to vote for Ahmadinejad and take members of their family with them to the polls. The rise of Ahmadinejad, himself once a member of the IRGC and reportedly an engineer in its infamous Al-Quds Brigade, has further encouraged the IRGC to seek an increasing share of political power.
It is difficult to imagine the IRGC quelling the current protests and then simply turning power over to the clergy. If a political compromise cannot be reached between the regime and the opposition, and the IRGC is used in suppressing the protests, its commanders would likely expect a bigger role in the government. It is even conceivable that faced with irresolution among the clergy, they will act on their own, and establish a military dictatorship that uses Islam as its ideological veneer–similar to Pakistan under Muhammad Zia-ul-Haq.
Khamenei thus finds himself in a difficult situation as a result of his incautious gambit with Ahmadinejad. Whether he gives more power to the IRGC or to the opposition, there is little chance that he will emerge from the current crisis with his supremacy intact.