Your statements here and the article you linked to offer up a lot of speculation derived from observable facts. Assuming each step in the chain to full on arms race is going to happen and the continuing spread of this technology to places in all directions of the compass outside of the Middle East what can we possibly hope to do to stop this?
Assuming it is impossible: How does a Persian - Arab arms race evolve differently than a Soviet - USA arms race or Pakistan - India arms race? The two that have actually happened seem to develop into largely peaceful posturing, grumbling and proxy warfare.
This future you describe honestly does not seem different than today: Iran uses its proxy forces to control various parts of the Middle East. The populaces of most countries that can really go to war with Iran have no stomach for it. Their governments can probably only perform air strikes or missile strikes - so it’s not different whether Iran has or does not have nukes.
I have faith in Iran’s people so long as they remain as free as they are now. I think the enhanced education of the populace in pursuit of various types of technology, even in weapons, will tend toward opening up their society. I think a large part of what is driving the revolutionary forces in the Middle East, from terrorist to Arab Spring, is a population of well-educated, motivated individuals with little to no opportunities.
Whether your scenario or a scenario without Iran nuclear weapons comes to pass, attempts at peaceful, non-punitive diplomatic activities will have the best outcomes for us in the long run.
Although it is valuable to develop the kinds of techniques exhibited by Stuxnet, I think it is a half measure and does not, in the long run, serve our goal: an Iran free of nuclear weapons.