Entering Iran from Iraqi airspace would be politically delicate. Although U.S. troops are no longer there, traversing Iraqi airspace would not be possible without the knowledge, and most likely the permission, of the United States.
The key question is whether Israel's fighter-bombers can conduct this mission without refuelling. Combat radius - the distance an aircraft can fly and return without refueling - is difficult to calculate, and depends on weapons payload, external fuel tanks, mission profile, etc.
The best "guesstimate" of the combat radius of the F-15I and F-16I, outfitted with conformal fuel tanks, two external wing tanks and a decent weapons load, is almost 1,609 kilometers. Either of the two possible flight routes above is about 322 kilometers further than that. To make up for the shortfall, the aircraft could be fitted with an additional external fuel tank, but this will require a reduction in the weapons load. Given the accuracy of the weapons in the Israeli inventory, that might not be problematic.
However, if the aircraft are detected and intercepted, the pilots will have to jettison the tanks in order to engage their attackers. Dropping the tanks will prevent the aircraft from reaching their target.
Air refuelling is a limitation for the Israelis. In recent years Israel has acquired five C-130 and four to seven Boeing 707 tanker aircraft. However, the tankers would have to refuel the fighters in hostile airspace. The 707 is a large unarmed aircraft and would be very vulnerable to air defences.
Theoretically, the Israelis could do this, but at great risk of failure. If they decide to attack Natanz, they will have to inflict sufficient damage the first time - they probably will not be able to mount follow-on strikes at other facilities.
The ultimate question, of course, is once Israeli planes have flown back, won't Iran be able to repair the damage and accelerate the nuclear programme? Or does Israel assume that the U.S. will pick up where they left and start a long-term war with Iran?