Phil Johnson wrote a great article for Pulpit Magazine about the Wrong Kind of Unity as it applies to Catholicism. I like that he not only dealt with the disunity in Roman Catholicism, but whether organizational unity is a quality to be desired in the first place.
“When Jesus prayed that we all might be one, He was describing a spiritual unity. In John 17:11, He prayed “that they may be one, even as We are.” Verse 21 continues: “that they may all be one; even as Thou, Father, art in Me, and I in Thee, that they also may be in Us” (emphasis added).
That describes a very specific kind of spiritual unity that proceeds from our union with Christ. Christ Himself likens it to the unity between Father and Son. It is certainly not something as mundane and superficial as the homogenization of all churches under one earthly hierarchy of bishops in Rome or Constantinople.”
Catholics tend to use the verse above to bolster their argument that Jesus wanted organizational unity and that the “splintering” of Protestant groups goes against the desires of Christ for his church. Not only is this argument flawed in its premise, but it is an argument that works against the Catholic Church itself.
“Organizational unity cannot guarantee true spiritual unity, and the proof is seen in the Church of Rome herself. Despite all the Catholic finger-wagging about the lack of unity reflected in Protestant denominationalism, there may well be more disharmony within the Roman Catholic Church than there is in the typical Protestant denomination.”
From here, Phil goes on to give examples of disharmony among some more well-known Catholic apologists like Keating against Matatics and Sugenis against Keating, citing online documents of these battles and other battles amongst the members of the Roman Catholic Church. Phil makes the point that the Roman Catholic Church is certainly a far cry from the unity seen within the Trinity that Jesus spoke about.
Finally, Phil describes the type of unity that Christians should strive for:
“But the unity Scripture calls us to is a unity in truth. Paul wrote, “Now I plead with you, brethren, by the name of our Lord Jesus Christ, that you all speak the same thing, and that there be no divisions among you, but that you be perfectly joined together in the same mind and in the same judgment” (1 Cor. 1:10). He did not counsel the Corinthians to grasp for a superficial unity by setting truth aside and embracing an organizational unity without regard to sound doctrine. Nor did Paul order them to abandon their differences and simply place a blind and implicit trust in his apostolic magisterium. He was urging them to work through their differences and strive to achieve unity in both heart and mind. Such unity is possible only when people are themselves in union with Christ. “For who has known the mind of the Lord, that he will instruct Him? But we have the mind of Christ” (1 Cor. 2:16).”
We should strive for truth and sound doctrines, not organizational unity. If we are truly in Christ, then we are truly unified.