One of our biggest hero's of faith is the apostle Paul. Someone who in the days after Jesus was persecuting and killed Christians because of his own beliefs. It wasn't until he himself was struck down be Jesus himself with MERCY, did he realize what he was doing.
People could have prayed all they wanted for the people being killed by Saul (Paul before he was changed) but the problem wasn't them, it was with the persecutors.
What would it mean to pray for Isis? Would it mean accepting that God CAN actually work all things out for the good of those who love him? (Romans 8:28) Would it take a lot of faith? Of course it will, but I want to encourage other Christian's to lift Isis up to this prayer.
We pray right now, that your presence is in Iraq. That you will send a heavenly host of angels to protect the Christians fleeing and stuck there being tortured and killed. More than this, God we pray that the members of Isis will be struck with Mercy the way Saul was on the way to Damascus. Let their hearts and minds be transformed as they realize the evil that has consumed them. Let them find mercy in their eyes as they stare into the people standing for their faith. Let them be taken back by the love that pours out of these people to stand for you and your ultimate goodness. We know that you can bring good from anything, even if it seems unimaginable, but I pray all these things in Jesus' name.