Conflicts and challenges are bound to occur in any group, even Christian ones. The issue is not that churches have disagreements, but rather, how they deal with the disagreements that arise.
In his first recorded letter to Jesus followers of his era, the Apostle Peter gives these closing thoughts,
Finally, all of you, be like-minded, be sympathetic, love one another, be compassionate and humble.
He calls the church to pay attention to their attitudes towards one another in all of their dealings, knowing that if their attitudes are righteous, the outcomes of their disagreements will be as well. Pay attention to your attitude as you deal with brothers and sisters in Christ. A right attitude increases the likelihood of a right outcome and preserves the unity needed to walk the walk of faith.