WarSclerotic

Seems like if you’re willing to do a ballistic missile attack, an EMP strike would be a possibility. Short everything electrical in the whole country, essentially no fallout. Once the comm links are down (with the exception of fiber optics, assuming you don’t fry the electronics on either end of the fiber optic connections), the rest becomes much easier because the Iranians would be deaf and blind. Uranium centrifuges don’t run on squirrels, no electricity = no U-235 separation, and no live machine tools to make the bomb.
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Drawbacks include:
1. First use of nuclear weapons in space for offensive purposes, with all attendant international legal and political opprobrium.
2. Of all the systems likely to survive an EMP, the military stuff (SAMs, etc.) is probably the most hardened.
3. If I can think of this, so can the Iranians, and Faraday cages around sensitive and vital equipment are cheap compared to the bomb program as a whole.
4. Backup generators may be able to supply power for an extended period of time at critical facilities. It’s not as if Iran is short on fuel that a diesel engine can run.
5. This will brutally punish the Iranian population economically and in terms of convenience, and if they get riled then backing down from a bomb program is much harder for anyone who might succeed the current government.
6. Limiting the EMP effect to Iran may be difficult, meaning satellite dishes, cell phones and anything else electronic all over the Persian Gulf may go poof and further enrage countries who don’t like Israel, but don’t support the Iranian bomb program either, e.g., KSA, Qatar, Dubai, etc. It may be easier to get overflight rights on the DL than force them to replace anything electronic. Not to mention the US armed forces, who are nominally Israeli allies and might have systems fried as well.
7. Western countries have much more to lose in an EMP exchange, this includes Israel.

OK, so there’s a lot of downside. But it’s still short of popping full thermonuclear devices over these places, and it dramatically lowers the risk to Israeli pilots. Breaking the Iranians’ stuff would be a setback, to really tank the program you need to get the people who run the program, and that requires excellent intel and boots on the ground. That is a much bigger investment than flying multiple sorties.