There is a difference between a God-ordained, separation among believers for the purpose of following our individual conscience before God and a division birthed out of anger and pride.
In the Old Testament, God raised up a holy people through which to bring forth the righteous Branch of David; in the New Testament, He has promised to raise up a bride without spot or blemish, a holy people perfectly unified and conformed to one another by the love of Jesus.
Notice, it is His faith and love that perfects–His heavenly wisdom and pattern that prevails–and the work of His Holy Spirit that authors and finishes our faith.
Everything is of, by, and through Him.
Yet, consider the challenges that believers face in living in unity with one another today: the body of Christ is divided; and believers around the globe are in various stages of agreement with one another concerning how God has called us to practice our faith.
As God builds His church, we must acknowledge that these divisions are not principally disagreements, but rather, differences in discernment.
Moreover, we know that God is faithful:
When He is ready, He will remove every foul thing from among us.
We will be perfectly unified as one body in doctrine and practice.
Then, that which is perfect will come.
To expect any less than this is not our reasonable and expected level of faith–for we are called to believe that He is able to succor and unify His people.
Yet, a practical dilemma remains:
How can we mediate our differences in doctrine and practice in a way that best exemplifies that we are one body in Christ [and members of one another]?
How can we mediate these differences without violating our conscience in the private and corporate practice of our faith?
These things shall guides us, as they lead to peace:
Each man is accountable before God for his own conscience and manner of life: therefore, regarding the private practice of our faith, we are not to judge one another in disputable things [areas in which God allows us to exercise personal discretion].
We should never ask or expect another believer to act corporately in a way that contravenes their faith: for we are called to follow Christ, not man.
The fact that God has made room for our differences does not suggest that there is such a thing as a private interpretation of scripture–for Jesus showed us how to walk perfectly in this world and His apostles established consistent customs in every assembly–but rather, that He permits us to follow our individual conscience.
Pray, meditate, and act, as God leads: this is the way of a conscience conformed to Christ.