The "two military assistants" of Khamenei are irrelevant. The nuclear weapons program has its own dynamic, and Parchin, Qom, and Natanz are not the only sites of weaponization. There are a hundred or more such places in the disseminated, complex underground web of bunkers, civilian-covered facilities and so on.
4 UN peacekeepers injured in Sinai and taken to hospital in south Israel (Haaretz)
from the article: An inside look at the base where Iran is developing nuclear weapons