I believe it does.
Think about it, people. The problem lies in the fact that we think just in terms of extreme examples that are hard to realistically relate to unless we've had first hand experience(bombs, threats, violence, rape, torture). So, I'll try to give it a better shot, and I think people may, hopefully, find themselves agreeing with me.
I'm from Hermosillo the capital city of the state of Sonora, in Mexico. Being the capital we understandably have the same problems that most capitals in our country face, but those are in our case mainly the uncheckered growth of our city, which translates to population, too, and the lack of water. We are always trying to find ways to get more water.
Now, bear in mind that we are a third world country, and that with the growth of the city comes the growth of unwanted individuals, in the case of my example: children, many who will end as street children, children that will most likely one day grow up to stab you to take money to support their drug habit, rape you, or just kill you.
Also, there is in the city, an orphanage named Kino, after a priest from a while ago. Said orphanage is run by a church, one of those places with funnily dressed people who put the fear of God in ya, and also the same people that are clothing, feeding, nurturing, and putting a roof over the heads of many children, and ALSO putting them through school.
Now, I'm a naturalist and rationalist, and you could rightfully call me an atheist, and I believe that when I look at the state of things, human affairs, from a broader perspective; religion, in general, is one of the biggest tragedy to ever befall mankind, just behind extremism; and YET, I'm all for those people taking those children in and putting the fear of God in their hearts because the alternative is much, much worse, and I also think that it is very respectable of the priests to do that. The kids one day will grow up and some will have a shot at having a decent life, and they will deal with their fear of God pretty much the same way everyone does it, and that will be how things will go.
So, yeah, the end does justify the means. No matter how you slice it.
The only issue how you understand the justification and in what context it comes from.