Killing the ayatollah would simply cause the state to collapse, and a civil war to break out.

To that end, I thought Victor Davis Hansen had an interesting read of exactly how "regime change" would shake out in Iran with the current state of things we know on the ground.

The TLDR being that the people of Iran will absolutely be embarrassed and angry over the impotence of their leadership after what has happened, but lacks the organization to be able to do anything about it themselves. With what he saw as more likely being that the Military (which has now seen all of its own regime-friendly officers killed and replaced by younger "wild card" officers) will take the opportunity to blame the Ayatollahs for this mess, execute them, and implement an Egyptian-style Military Dictatorship. Which he also views as only marginally better than the current situation in terms of regional stability.