So to get specific. The weapons factory (or storage facility, or port facility-airport-reshipment center) is a legitimate military target, and the civilians who work they are not strictly non-combatants: they are directly contributing to the military effort. When you hit that target and they are injured or killed, it's not murder.
The people that run the lunch cart, the children in the house near the factory? The child who unluckily happens to be in the house when we finally track down Bin Laden? They are innocent: but you are not intentionally targetting them. Our military, the Israeli military (to mention two militaries who strive to uphold a just warrior ethic) would take steps to try to minimize these deaths if they can; but if they're caught in the crossfire, so to speak, that's collateral and that's not murder.
And as you know, our military would try to medevac them out and save their lives, if they can.
Those unintended injuries and deaths are not the same as murder. These deaths are foreseeable (though not intended) especially when you're fighting an enemy that operates out of residential neighborhoods, blends in with noncombatants and uses civilian shields. Once again, a good military may well end up leaving a trail of collateral damage inthat kind of situation which was NOT intended and which they strained every muscle to minimize.
What's not justified is: (1) deliberately targetting the "innocent," the non-combatants; or (2) deliberately choosing WMDs which cause indiscriminate destruction to "whole cities or vast areas with their inhabitants." That is quite different from collateral deaths. That, strictly speaking, constitutes a crime.
Hiroshima and Nagasaki and while we’re at it, Dresden, were all legitimate strategic targets.
All of which were a total military success that achieved their objective.
I like your Pope. I liked the last one too. But he’s wrong on this. It happens.