Shahzeb Shaikha is certainly not incorrect in setting out his views on the prospects of a nuclear armed Iran on Pakistan's door-step.
Shahzeb has discomfort with Iran's "peaceful" nuclear program, and justifiably so. Undoubtedly, Iran's nuclear program may be peaceful in intent; but will not necessarily be confined to that. There is a reason for that- Iran is and will be viewed with doubts by many quarters in the world and hence justifiably needs to have a nuclear capability. And the Iranians have single-mindedly and fiercely pursued a foreign policy of their own. To sustain that, they need to have a nuclear option.
Then Shahzeb says something which is a fact- "The interests of Pakistan and Iran clash in Afghanistan, and Irans relations with our key ally in the Middle East, Saudi Arabia, remain rocky." Indeed there is no congruence between Pakistani and Iranian interests in Afghanistan whatsoever (apart from seeing USA out of there). And the Saudi involvement in Pakistan affairs is something that Iran abhors, and that is something that will never change. Actually, Iran even views Pakistan as a Saudi instrument just as it sees (?)/saw Pakistan as an American instrument since the advent of the ayatollahs. That is precisely what Shahzeb is pointing towards.
Shahzeb also says- "In addition, Indias improving relations with Iran is also mind-boggling for our India-centric attitude and policy." While this is true, its not a permanent given. Simply because, firstly: Iran has to remain pragmatic in its outlook. It needs to have some (at least neutral) countries to deal with. India is one such, India has had a relationship with Iran that is historically neutral to friendly. Even if India becomes unfriendly, it can do little harm to Iran in any way; that is what is clear to Iran. Iran does not view Pakistan the same way, esp given Pakistan's relationships with KSA and USA. So Iran will use Indo -Iranian relations as some kind of counter-balance. Not to mention economic considerations in these sanction-ridden times.
Iran's sectarian views and requirements are vastly different from Pakistans (nothwithstanding the "one ummah" concept). Shahzeb has noticed that and pointed that out in his piece. Will that difference ever be eliminated? We ought not to forget that in the countries involved i.e. Iran, Pakistan, KSA: even religious ideas are involved in setting up foreign policies and that will not change. Though one might say that Pakistan may be slightly less similarly driven, the stance that Pakistan has steadily taken since the Zia era; Pakistan's foreign policies will likely take a greater theocratic hue in times to come. Which is alright, except that there again; there will not be any congruence with Iran.
Just as Pakistan believed that she had the right to posess an "Islamic Bomb", Iran also believes she has the right (and necessity) to posess a no less "Islamic Bomb". Now with the evident sectarian divides and fault-lines; will that "Islamic Bomb" gain another moniker remains to be seen. Does Shahzeb Shaikha believe that will happen?