In Dark Sun, Richard Rhodes reports on a speech by Curtis LeMay, who commanded the the bombing of Japan's cities during World War II. LeMay reported on an analysis of Japan's three possible defenses to this bombing. One was fighter and aircraft defenses, but, LeMay noted, no U.S. attack had been turned back in this way during the war. A second was destruction of the U.S. bombers at their bases in the Marianas, but this would not have worked because even one bomber with an atomic bomb would have done the work of hundreds, and because U.S. industry would quickly have replenished the supply of bombers. The third was destruction of the U.S. factories and laboratories that were producing the bombs. This would have worked, but Japan had no means of getting to them.
The Israelis certainly do not want to try defending against atomic-tipped Iranian missiles. Destroying Iranian bombers at their airfields and Iranian missiles in their silos (eventually) or on their launchers, shows more promise, but does not provide the certainty required by Israel. This leaves destruction of the factories and laboratories producing the bombs.