Many a fool has pointed to disagreements in Church denominations and made some claims as to disagreements equalling irrelevance or worse. First of all, unity does not mean uniformity. Right from the beginning there were different forms of worship. The unity that Jesus demands is in worshipping Him as Creator and Saviour of the universe, regardless of the form that worship takes.
And regardless of what people think, those who have been born again into faith in Christ via the leading of God and the transforming power of the Holy Spirit are one in Christ. In my opinion, the many different denominations simply reflect the diverse nature of humans and the dynamic power of Christianity. Jesus relates to all people in all times in all cultures. The Bible appeals to different people in different ways, and Jesus says that in heaven there will be people from every language, race and tribe.
On the other hand, our fallen nature dictates that we see ourselves as right and others less so. This is wrong, and atheists are correct to criticize this fault in human nature, theirs included.Paul understood that peace and unity cannot exist apart from the truth of the Gospel. To compromise the Gospel of truth would be to lose what creates our unity and peace. When a decision must be made between unity and truth, unity must yield to truth; for it is better to be divided by truth than united by error. We test the church by truth, not truth by the church.