Israel can detonate some small nukes in the ionosphere and fry all the electronics in a sizable area within Iran. That wouldn’t kill the civilians, but would render a response from Ahmadinejad impossible.
“..fry all the electronics in a sizable area within Iran.”
And possibly electronics of airplanes in flight and equipment needed by our spies within Iran. Bad move.
EMP has never been effective against military targets, even their mostly geriatric ones which are still semi-hardened. If you're close enough to a military target to damage it with EMP you're close enough to damage it with high explosives. Also not clear if Israel has the specialized EMP warheads, and if they used large general purpose warheads in the atmosphere, well, the whole world would then be at war with Israel.
That wouldn’t kill the civilians, but would render a response from Ahmadinejad impossible.
You're forgetting what embedded cells overseas can do even if the EMP thing worked (it won't).