The power of church government is to determine matters based on the authority given to her by Christ himself and based on the instructions he has given her in Holy Scripture. Church power is ministerial and declarative, not magisterial or legislative. That submission which Christians owe to the human government of the church is free from all dogmas, dictums, and decrees, which are in any way contrary to Scripture, and in matters of faith or worship, from anything beside them (i. e. not contained in the Scriptures,) as the assembly of divines at Westminster so ably summarized in their chapter on Christian Liberty and Liberty of Conscience:
XX.II. God alone is Lord of the conscience, and has left it free from the doctrines and commandments of men, which are, in any thing, contrary to His Word; or beside it, if matters of faith, or worship. So that, to believe such doctrines, or to obey such commands, out of conscience, is to betray true liberty of conscience: and the requiring of an implicit faith, and an absolute and blind obedience, is to destroy liberty of conscience, and reason also.
The elders of the church must take care to protect the liberty that Christians have to obey God in his word. Although submission to the elders of the church is required of all Christians, this submission is not limitless, but is “in the Lord”, meaning that it is only based on the Lord’s authority as he has revealed himself in his word, and that Christians are not to submit in matters which they do not believe to be coming from the word of the Lord. To submit to human authority against ones own conscience in matters of faith or worship is sin, for anything that is not of faith is sin (Romans 14:23), and the Christian is required to “obey God rather than men.” (Acts 5:29)
Even as Christians are obligated to do everything in their power to keep the peace and unity of the church, as far as it lies within them, even so the elders of the church are not to proceed in a way that puts pressure on Christians to sin against their conscience, even in matters in which they may need to be corrected. In such cases, the elders may determine that the individual Christian’s belief is not only unwarranted by Scripture, but also potentially divisive to the church, and for that reason cannot be allowed. In that case the elders of a particular church would counsel the Christian to unite with another body whose beliefs are more in line with his scruples. It is also entirely appropriate for the elders to continue to seek to persuade the Christian that that which he has scruples about is not in fact a sin, or that he is incorrect, based on the teaching of Scripture, and that he should change his thinking on the subject. It is entirely inappropriate, pernicious, and does violence to that liberty which Christ purchased for the Christian on the cross, for the elders to require or even suggest that the Christian submit to their authority against his conscience despite his scruples about a given matter of faith or worship. That is equivalent to asking the Christian to sin, which elders in the church are never permitted to ask. (Yes, this applies to individual pastors, too.)