Many times we hear that war is wrong from a "Christian" perspective, because it breaks the commandment that says "Thou shalt not murder". Such an absolute statement creates obvious problems. For example, what does a Christian do in the case of being attacked by another nation or, as is currently the case, by a group of people bent on destroying your country?
The Biblical view of war may surprise many. Let's start with the language. The verb used in Exodus 20 for "murder" is never applied to Israel at war, and applies only in cases of premeditated killing of other individuals.
We all agree that judgment is God's alone, and that we should treat our enemies with respect and love. However, I hope we also agree that according to the Bible, we know the difference between right and wrong, and what justice constitutes according to God.
We learn this from Scripture:
"Romans 13:1-5 (NIV)
Everyone must submit himself to the governing authorities, for there is no authority except that which God has established. The authorities that exist have been established by God.  Consequently, he who rebels against the authority is rebelling against what God has instituted, and those who do so will bring judgment on themselves.  For rulers hold no terror for those who do right, but for those who do wrong. Do you want to be free from fear of the one in authority? Then do what is right and he will commend you.  For he is God's servant to do you good. But if you do wrong, be afraid, for he does not bear the sword for nothing. He is God's servant, an agent of wrath to bring punishment on the wrongdoer.  Therefore, it is necessary to submit to the authorities, not only because of possible punishment but also because of conscience. "
Here it is written that God has delegated some of His authority to the government, and as such, the government has the right to pursue wars against evil and to administer justice. The passage above gives the government the right to bear the sword against these people.
God wills that human justice hold sway among governments, and between citizens and civil authority. He does not prescribe that governments always turn the other cheek. The government "does not bear the sword for nothing." Police have the God-given right to use force to restrain evil and bring law-breakers to justice. And legitimate states have the God-given right to restrain life-threatening aggression and bring criminals to justice. If these truths are known, this God-ordained exercise of divine prerogative would glorify the justice of God who mercifully ordains that the flood of sin and misery be restrained in the earth.
Is it not our Christian duty to protect the innocent? Do we just let evil steamroller over us? We are citizens of 2 kingdoms, the heavenly and the earthly, and we should follow what God tells us to do in both cases.
"1 Peter 2:13-14 (NIV)
Submit yourselves for the Lord's sake to every authority instituted among men: whether to the king, as the supreme authority,  or to governors, who are sent by him to punish those who do wrong and to commend those who do right. "
This verse confirms the earlier verse from Romans, while adding that these authorities appointed by God are the ones that punishes those who do evil. And the instruction is clear, we must submit to them for the Lord's sake. So if you are required by your government to go to war, you should submit to that, provided that it is a just war.
It is very important, however, to remember here the distinction between church and state. The Christian fights in a war not as an ambassador of the church or on behalf of the church, but as an ambassador of his country. The church is not to use violence (John 18:36), but the government at times may (John 18:36; Romans 13:3-4; etc.). So the Christian fights not as an agent of the church, but as an agent of the government of his country. Both are ultimately under the authority of God, but each has a distinct role.
What, now, are we to make of Jesus' radical commands in Matthew 5:39-41? "Do not resist him who is evil; but whoever slaps you on your right cheek, turn to him the other also. And if anyone wants to sue you, and take your shirt, let him have your coat also. And whoever shall force you to go one mile, go with him two." How does this fit with what we have seen above?
First, we need to clarify what the problem is not. The problem is not that Jesus appears to be telling us to lie down and let evil overtake us. That is clearly not what he is saying. Instead, he is telling us what it looks like "not [to] be overcome by evil, but [to] overcome evil with good" (Romans 12:21)
So the problem is not that it looks as though Jesus is telling us to let evil steam-roll over us. The problem is that it looks like Jesus is telling us that the only way we should ever seek to overcome evil is by letting it go and responding with kindness. It looks as though he leaves no place for using force in resisting evil.
Part of the answer to this difficulty lies in understanding the hyperbolic nature of much of the Sermon on the Mount. I don't think that Jesus is telling us never to respond to evil with force (such as in self-defense) or always to literally turn the other cheek when we are slapped any more than his command later in the Sermon on the Mount in Matthew 6:6 means that we should only pray when we are completely alone or his command in 5:29 means that some should literally gouge out their eyes. Jesus himself drove the thieves away from the temple with a whip (John 2:15) and Paul at times insisted on his rights as a Roman citizen (Acts 25:11; cf. also the interesting instance of 16:35-40). Jesus is using hyperbole to illustrate what our primary disposition and attitude should be, not to say that we should literally give in to every attempt to do evil against us. That is part of the answer.
The main part of the answer, however, lies in remembering that Jesus is speaking primarily to individuals. He is not mainly addressing governments here, but is primarily speaking at the personal level. This text, then, shows that an individual's primary response to evil should be to "turn the other cheek," while the other texts we have seen (e.g., Romans 13:3-4) show that government's God-given responsibility is to punish those who commit civil crimes (murder, terrorism, acts of war, etc.). While it is sometimes appropriate even for individuals to use self-defense, it is never appropriate for individuals to seek to punish others. But it is right, however, for governments both to take measures of self-defense and to execute retribution.
There are, in other words, various "spheres" of life. God has willed that some spheres include responsibilities that are not necessarily included in other spheres. Personally, it would be wrong for us to execute retribution on people who harm us. But passages like Romans 13:3-4 and John 18:36 show that Jesus is not denying governments the right to execute retribution on evildoers. Therefore, when a Christian is under the authority of the government and authorized to fight in a just war on the nation's behalf, it is appropriate for him to fight. For he is not fighting as a private individual, but as a representative of the government to which God has given the power of the sword.
I want to add a piece here about the just war criteria, since this is what defines the cases under which war can be justified. It was written by Augustine (no relation )
1) Proper Authority - Augustine meant by this that war is not to be waged by private citizens but rather by properly constituted governments.
2) Proper cause – We are not to go to war for revenge nor as Augustine put it ‘the lust for dominating’. The primary reason for going to war is self defence.
3) A reasonable chance of success
4) Proportionality - This has come to mean that non-combatants should be kept from harm, as far as possible.
Therefore, we will magnify the mercy of God by praying for our enemies to be saved and reconciled to God. At the personal level we will be willing to suffer for their everlasting good, and we will give them food and drink. We will put away malicious hatred and private vengeance. But at the public level we will also magnify the justice of God by praying and working for justice to be done on the earth, if necessary through wise and measured force from God-ordained authority.