Nuking Israel

A reader makes a point I've long wondered about:

The point made by Goldfarb about deterring Iran by threatening the holy city of Qom got me thinking: how on earth could a government like the one in Tehran expect to destroy Israel without destroying Jerusalem, the third-holiest city in Islam? Even at his blustering worst, Saddam Hussein only threatened to incinerate "half" of Israel because he knew he could not attack Jerusalem. Does Netanyahu really believe than an Iranian government bent on becoming the leader of the Muslim world would risk incinerating a city holy to Muslims like Jerusalem? Why not launch nukes at Mecca and Medina while they're at it?

Are the Israelis crying wolf? Is that wise? Or is this so unknowable that their existential anxiety is as understandable as it is tragic?