While there are just and unjust reasons for waging war, “just war theory” has become a catch-all phrase for leftist and pacifist claptrap often coated in gooey heretical religiosity.
On the subject of "Just War" and nuclear weapons, I once ran across an excellent book on the topic:
A Fighting Chance: The Moral Use of Nuclear Weapons.
It's long since out of print, and is written in the context of the cold war between USA and USSR. Still, it's an excellent study of a real-world problem, and as such is timeless. As I recall, the author is a retired USAF officer, a Catholic, and might be a FReeper.
Let's just say that his analysis is different from that of the pacifist bishops.