I'll post my own stuff before Mosh answers... BUT...
The thing that makes me appreciate this song as much as I do is the fact that willingly or unwillingly, 'Arry is criticising the religion... from the viewpoint of a religious man. You see, believe it or not, Christianity (and a whole lotta other religions as well) are built upon love, peace and understanding. As one of my favourite preachers says, "You should behave like Christ, meaning everyone should feel good in your presence. Everybody should be cool with you and you should be cool with them." That's one of the core beliefs.
Of course, there are reasons to lead a war, but these are often overstated and downgraded into a petty infighting. You say you are fighting "in God's name", "for the greater good of God", yet you are only making yourself feel better and you are taking Lord's name in vain - not by saying "Oh, Jaysus, I did this and this", but by taking His name and coating your own agenda with it.
Are you a man of peace
Or a man of holy war
Holy war probably has its place, but the way it has been used in the past years, it's definitely blasphemic, in anyway.
Too many sides to you
Don't know which anymore
Since these people use their own reasoning and their own, human logic and then they pin "God's will" tag to it.
So many full of life
But also filled with pain
Don't know just how many
Will live to breathe again
This shows the hypocrisy - whether your religion of choice is Christianity, or Islam, or Judaism or even Atheism (more in line with Humanism, you get what I mean) - your goal should be understanding, feeling for your brother, the other human and supporting the weak, trying to live out your true potential. Mass murdering the others is always a weird way to achieve this.
A life that's made to breathe destruction or defense
A mind that's vain corruption bad or good intent
A wolf in sheep's clothing
Or saintly or sinner
Or some that would believe
A holy war winner
This again plays with the appearances these "holy warriors" try to maintain... only to be vile and corrupt and not mindful of God's plans. (You can also transpose this into everyday life - you have these "fighters for the higher good", even if it might not be a war itself)
Please tell me now what life is
Please tell me now what love is
Well tell me now what war is
Again tell me what life is
This juxtaposition Mosh has talked about is explicitly mentioning that faith (and religion, believe it or not) should be about life and about love, about creation, not about destruction. Evil is only a corrupted good - you can always argue the good out of the bad (is there really a person who would actually like to be lied to, deceived, betrayed? That is, would anyone want pure evil? And if not, are the evils of this world not merely good went astray? - I kill a person in order to have his money -> buying something -> pleasure, not because it's bad - )
More pain and misery in the history of mankind
Sometimes it seems more like the blind leading the blind
It brings upon us more of famine, death and war
You know religion has a lot to answer for
This seems like criticising religion, but to me, it's mostly about criticising wrong religion, or - more precisely - the "I" religion.
And all because of it you'd think that we would learn
But still the body count the city fires burn
Somewhere there's someone dying in a foreign land
Meanwhile the world is crying, stupidity of man
Tell me why, tell me why
'Arry is asking about the futility of war, of conflict, in order to bring peace, love, the "good" result. And failing. It's true, there is no answer.
He gave his life for us, he fell upon the cross
To die for all of those who never mourn his loss
It wasn't meant for us to feel the pain again
Tell me why, tell me why
This is specifically from a Christian's point of view (I see no other interpretation, honestly) and it sums up the meaning of this song in four simple lines. Nuff said.
Again, I tried to write this down now and quickly, sorry for any inconsistencies or anything.