This is a true ideological crisis for the Revolution. The government can crack down on dissenters of all stripes, but they can't very well declare that a government based on the Guardianship of the Clergy can crack down on the most esteemed clergy in the country. They can't issue some edict that will change the very nature of Shi'a Islam so that the people no longer show deference to their own Grand Ayatollahs.
Yet, the government still maintains all the levers of coercion. The question is: will the rank-and-file members of the armed services, Revolutionary Guard, and Intelligence Services obey the Supreme Leader when he is opposed by a religious establishment that has much greater religious legitimacy?
More Iranian Rumblings
Booman does a good job of explaining why Rafsanjani's successful wooing of the clergy at Qom is so potentially dangerous to Ahmadinejad's regime:
It took about two years for things to build up enough to topple the Shah. I have a feeling it won't take quite as long this time.