I ask this question because some Bible-believing Christians feel that prayer for peace in these "last days" would be contrary to God's will, since Jesus said, "When you hear of wars and rumors of wars, do not be alarmed. This must take place, but the end is not yet" (Mark 13:7). If war "must take place," how can you pray for peace without opposing God?
Our prayers should be guided by what is morally right for men to do, not by what God, in his sovereign providence, may will to take place. Rarely, if ever, should we pray for moral evil to take place, but God may will that moral evil prevail for a season. For example: 1) God willed that Christ be crucified. Many of the necessary acts involved in crucifying Christ were morally evil. Therefore, God willed that this moral evil prevail for a season (Acts 2:23; 4:27-28). 2) God willed that Joseph's brothers sell him into slavery in Egypt, even though this was evil for them to do (Genesis 50:20). 3) And God ordains the sinful ravages of the end times (Revelation 17:17).
In other words, God ordains and predicts that moral evil prevail for certain seasons, but this does not mean we should pray for moral evil to happen. We should pray according to the way God has commanded us to live - in righteousness and love. We should pray that God's will be done on earth the way it's done in heaven by the perfectly holy angels (Matthew 6:10), not the way it's done on earth through the agency of sinful men.
In fact, Paul teaches us to pray for peace among nations for the sake of the gospel. The crucial text relating to prayer and peace is 1 Timothy 2:1-4. "First of all, then, I urge that supplications, prayers, intercessions, and thanksgivings be made for all people, for kings and all who are in high positions, that we may lead a peaceful and quiet life, godly and dignified in every way. This is good, and it is pleasing in the sight of God our Savior, who desires all people to be saved and to come to the knowledge of the truth."
Notice the link between praying for 1) national leaders, 2) the preservation of peace and order, and 3) the "desire for all to be saved." There is a connection between 1) national leadership, 2) peace, and 3) evangelism and missions. It is true that the church may grow in times of hostilities and war. But it is also true that wars have devastated the church in many areas. It is not our business to decide the sovereign purpose of God in ordaining that some wars happen. Our business is to pray that justice, peace, and the proclamation of the gospel prevail. Our business is to pray that the Christian church not be complicit in national affairs as if nation and church were one. Ours is to pray that the church be seen as aliens in the cause of Christ-exalting love and justice with no supreme allegiances to any nation.
This leaves open the possibility that Christians might support a just war. God has given to the governing authorities the right to bear the sword (Romans 13:1-6). There are occasions when justice and love painfully call for military force for the sake of opposing aggression or liberating the oppressed. In such cases our prayers would be for the minimizing of misery and the speedy triumph of justice and the restraint of animosities and cruelties.
So let us pray for the love and wisdom and courage and power and fruitfulness of the church of Jesus Christ around the world. Let us plead that she would be distinct from all the nations and all the national and ethnic manifestations of pride. Let us plead that she would be a peace-making presence of salt and light everywhere. And that she would be unafraid to call every nation into question for the sake of justice and humility. And that Jesus Christ would be magnified as no national deity, but as Lord of lords and King of kings. And let us pray that all lords and all kings see this and humble themselves and make way for the Lord of glory.