In your oppinion this is the way a theocratic revolution in Iran would go. Perhaps if I wrote a story depicting how the revolution happens, it SHOULD go as per the story. Hence, the NES idea. Such as, my theocratic guy (Let's name him "Balls") makes an alliance with the generals, and they allow him to go through with the revolution, and they quickly consolidate the nukes for themselves. A majority of the people in Pakistan probably wouldn't be too opposed to a theocracy in their country.
Were we playing a simulationist NES, what is to be done in this situation? Void the story, because you, as mod, believe that this story isn't realistic? That destroys stimulation to write further stories, and really peeves off the player.
A majority of the people in Pakistan wouldn't be too opposed to a theocracy?...uh...whut...
I think that it's a legitimate concern that it 'destroys stimulation', but look at it from another point of view. Say the player is the king of Poland-Lithuania during the 17th century, and wants to get rid of that annoying Sejm and actually push real policies through. So what he does is write a story talking about how troops loyal to the King march in and dispose of the nobles, and how he's created a more centralized monarchy.
That is playing as a God on a tremendous scale. There's a bloody good reason that the King couldn't do that and get away with it. If a player writes such a thing into his orders, I'd be fine with it, running a Simulationist NES. But I would definitely have a civil war begin, because noble privileges can't just be wiped out without them trying to do something about it. There would also be consequences in the governments of neighboring states like Russia, Prussia, Sweden, and the Habsburg Empire if they were just standing idly by refusing to take advantage of this glorious opportunity sitting in front of their faces...perhaps some runaway military commanders or palace conspiracies... You can't just erase real-world difficulties via a story. Unless you do a bloody good job of explaining your reasons for why something should occur - which is why self-justification ought to be a part of orders in a Simulationist NES, and a reason for me coming out in favor of describing all diplomacy to the mod in orders - and have sufficient grounds for being able to argue the plausibility of something, the mod should respond to your plans with the appropriate consequences. I have no interest in seeing NESes in which, for example, an imperial North African state based on trade develops a xenophobic protonationalistic empire cult and magically manages to gain a citizen army despite the massive socioeconomic factors militating against same. It's ridiculous, it's not a reasonable proposition for alternate history, and it's too arbitrary to allow into a NES.
In the case of your Pakistan example, the characterization 'theocratic' and 'Iran-style' is pretty vague, IMHO; Pakistan is already to an extent a heavily Islamized polity in terms of law, at least as compared to, say, the United States. There really aren't any high-level clerics like there were in Iran to try to take the reins there, too...and the military would be heavily against such a move, and the military basically controls Pakistani politics. So in your story, 'making an alliance with the generals' would be treated as playing God on the part of the player, because there's no guarantee that that's how the military in Pakistan would act
at all. Perhaps the support of some of the higher military leadership could be coerced into a loose agreement, but it would be a minority, and a civil war would erupt if this Islamist revolution of yours were pushed very far. A civil war which, IMHO, your theocratic ruler would be unlikely to win. In addition, groups would emerge within India, the United States, possibly Iran (given the relations between them and Pakistan), Russia, and China at the very least pushing for some kind of an intervention, with attendant political consequences if they are ignored. So, essentially, the player would be allowed to go through their plan, but it would have the consequence not of establishing a 'theocracy' in Pakistan but of initiating at the very least civil war and at most global thermonuclear war.