Yes, that's the point, and why the Supreme Leader is having his personal militia shoot protesters dead in the street.
If the Ayatollahs are smart, they will ultimately move to protect their own existence by calling for a new election and installing Mousavi. That would end the uprising and they would cling to their power.
It looks like they’ve realized that their initial violent reaction was only strengthening the revolution, and it looks like they may — may — have stepped back. But Mousavi is apparently directly challenging the authority of the “Supreme Leader” now. If the Ayatollahs continue to resist the revolution, then they will be swept away. And it may — again, may — be too late for them to strike a bargain with Mousavi to give up some of their control in order to retain power, diminished as it may be.