As one counter to the nuke, might a god have some sort of future-vision when it concerns massive amounts of death? I imagine most of the gods are pretty invested in keeping their city and worshippers alive, so if they had some warning would be willing to intervene.
That way, if a god wants to destroy the city, they have to get cunning and set events in motion which are hard to stop with a simple snap of the fingers teleporting said nuke into the elemental plane of nuclear fission.