The unity of the faith is dependent upon unity of faith. While we have an objective unity with all who share one Lord, one faith, one baptism, Paul does on to say that there is another unity that we must grow up into.
There is a unity we must preserve, and there is a unity we must accomplish. Wisdom must direct all those who strive for this future unity because we are trying to do this in a world where we have enemies and adversaries. The New Testament is filled with the gatherings of God, and the divisions of God.
A shepherd wants the flock unified, but he does not include the wolves in this. To do so in the name of unity would only introduce, and that very quickly, a bloody and unhappy disunity. A doctor does not the body to accomplish any kind of unity with cancer cells. To strive for unity with cancer cells is simply another way of striving for a disunity of soul and body.
Unity is driven by a desire to love and please God, and to follow Him in whatever He does. If God is fellowshipping with someone, then so must we. If we walk in the light as He is in the light, we have fellowship with one another and the blood of Jesus His Son cleanses us from all unrighteousness. By the same token, if we walk in the light we find ourselves in conflict with those who do not like what light reveals. In a dark world, those who want to walk in the light are those who are asking for conflict.
So do not assume that conflict means unscriptural disunity. Do not assume that conflict means that you are being persecuted for righteousness’ sake. In short, do not assume anything, and turn back to the Scriptures with complete humility of soul. Trust the Lord. God is growing us up into a perfect man, and the process does not always look like we think it should look.