Israel could destroy Iran’s nuclear program by seizing control of a few select sites.
Neutron weapons detonated above the sites would kill everything out to a radius of a few hundred to perhaps a thousand yards. Drop in IDF troops, take control of the sites and after establishing shelter in case further neutron devices are needed then proceed to demolish the underground sites. The Iranians would not be able to approach the sites regardless of what they tried. Small neutron devices would kill them inside tanks, planes, whatever. rinse,lather,repeat as needed.
Bunker buster type nuclear weapons would not guarantee destruction of the sites. They would have to detonate at considerable depth and very very close to the underground bunkers. Only demolition teams would be able to guarantee destruction of the underground sites. Nuclear bunker busters would also create a huge radioactive mess when inevitably one or more blasts breached the ground. Neutron blasts would not physically destroy anything non-biological on the ground and would leave no radioactive contamination.
The neutron weapons could be launched by sub, plane, jericho missile or even by the IDF forces on the ground.
This type of attack would leave 2 Israeli subs free to roam and also the bulk of Israeli air assets would remain over Israel for protection.
Think Entebbe x 10,000
Dirty bomb their facilities and make them hot and unusable to safely work in. The threat of being exposed to high levels of radiation should put a damper on the Iranians to want desire to work there.