Even as we desire unity, there will be controversy within the church until Christ returns. Here is one wise way to pray when conflicts and divisions arise:
Gracious Father, have mercy on your children in disputes. We are sorry for any root of pride or fear of man or lack of insight that influences our stance in the controversy before us. We confess that we are not pure in ourselves. Even as we strive to persuade one another, we stand in need of a merciful Advocate. We are sinners. We are finite and fallible.
On both sides of the matter at hand, we take refuge together in the glorious gospel of justification by faith alone through grace. We magnify Jesus Christ, our Savior and King for all he has done to make us his own. We are a thankful people even in our conflict. We are broken and humble to think that we would be loved and forgiven and accepted by an infinitely holy God.
Forbid, O Lord, that our spirit in this struggle would be one of hostility or ill will toward anyone. Deliver us from every form of debate that departs from love or diminishes truth. Grant, Father, as Francis Schaeffer pleaded in his last days, that our disagreements would prove to be golden opportunities to show the world how to love—not by avoiding conflicts, but by how we act in them.
Show us, O God, the relationship between doctrine and devotion, between truth and tenderness, between biblical faithfulness and biblical unity, between standing on the truth and standing together. Let none of us be unteachable, or beyond correction. May the outcome of our dispute be clearer vision of your glory and grace and truth and wisdom and power and knowledge.
By your Spirit, grant that the result of all our arguments be deeper humility, more dependence on mercy, sweeter fellowship with Jesus, stronger love in our common life, more radical obedience to the commands of our King, more authentic worship, and a greater readiness and eagerness to lay down our lives to finish the Great Commission.
In all this, Father, our passion is that you would be glorified through Jesus Christ. Amen.