Funny that you mention this, I participated in a debate tournament in high school where the resolution for my event asked if the United States' intervention in the Middle East was justified. It basically boiled down to pro taking a "The ends justify the means" stance (for the life of me I can't remember the philosophic idea we used) while the Neg claimed that the substantial damage was too costly to overlook (the neg views were a lot more varied than that, but this was the most common).
At the end of it, after I researched both sides and debated them both, I realized that if you're looking at it from a moral standpoint, then really looking at the ends and the means is entirely useless. If you look at it at one side, it shows that there was severe devastation, innocent lives were lost, and entire countries were left with a severely damaged economy and an oppresive nation playing The Sims with their politics. If you look at the other, you see that a commander won't always know that there are civilians in the area, or he won't mean for a certain building to be destroyed, or sometimes you're left with the fact that if they didn't commit the actions then a much worse action would be committed (Like the atomic bombings in Japan).
In the end, I find that if you want to look at what's morally correct then you have to look at it from an analysis of intent rather than results. Was it a moral action to bomb a building containing only civilians? Well that depends, did the commander ordering the strike know that there were civilians or was he told there were only soldiers? Was it moral for the soldiers to outlaw public expression in an occupied city? Well that depends, was the intent to oppress their rights or to keep public unrest at a minimum? In the end it's still difficult to determine morality, but it makes it slighlty more possible to define a moral action from an immoral action, even if you still have to go by a case-by-case basis.
If you're looking at it pragmatically, then you have no choice but to weigh the ends versus the means, this is just my moral view on it.