One more point on this whole matter. There has been some sort of confusion by friends of the Presbyterians Together document on why some have been claiming that the place to settle doctrinal issues is in the courts of the church. On more than blog I have read the claim that the church's courts are a last resort for those who can't resolve their issues peaceably.
But this claim betrays a lack of understanding of the basic principles of Presbyterian polity. One of the key principles of that polity is this: I, as an individual minister, have no authority to declare doctrine on my own. Rather, it is only as the church is gathered in its "courts" is there any authority to exercise "judgment," which includes not only discipline, but also the duty of declaring doctrine.
This is what the PCA Book of Church Order covers in chapter 3, "The nature and extent of church power (or authority)." The BCO makes the point that ecclesiastical authority is exercised in two ways: there is the power of order, which is exercised "severally" (or individually) under a grant from presbytery; the power of order covers things such as preaching the Gospel, administering the sacraments, and exercising pastoral care. And there is the power of juridiction, which is only exercised jointly as church courts (BCO 3-2) and covers matters such as doctrine and discipline (BCO 13-9, 14-6). In both instances, I only have authority as a minister as it is granted or exercised with other presbyters who exercise oversight over a larger part of Christ's church.
This is why when candidates for ministry apply for membership in our presbyteries, they appeal to the presbytery allow their scruples of conscience in reference to the Westminster Standards. Presbyteries have the authority to determine whether such scruples conflict with the Standards (BCO 21-4). As a private individual or as a single minister, I have no authority to determine that on my own for my brothers. We must hear the presbytery's voice on the matter as they rule "jointly" as a church court.
And so, far from being a "last resort," the church's courts should be the first place we go when we begin to raise biblical or theological issues that appear to raise questions about a church's consensus on certain doctrinal matters. This is the case for two reasons: we can't trust our own understandings on these matters for we may be self-deceived; and we must hear the voice of the church on matters of doctrine and discipline.
After hearing the church's voice, it may be that our consciences are convinced that the Word of God teaches a contrary position to the declared doctrinal position of the church; and if so, then we have to determine one of three actions: whether we will seek to change the church's consensus by working to see the church amend its doctrinal standard; whether we will submit to the brothers; or whether we will follow our consciences into a different church communion.
Whatever may be the case, we must begin to deal with these issues in a Presbyterian fashion. And that means we must demonstrate our commitment to love for our brothers by bringing these issues to the notice of the larger church in ways appropriate to our polity. And it also means that we need to forsake our understanding of the church's courts that appears to be drawn from American jurisprudence (i.e., as litigious bodies of punishment) and view them instead as the place where God's Spirit dwells to guide the entire church in matters of "judgment," which include the weighty doctrinal matters under discussion today.
[BTW--the best single source for understanding Presbyterian polity remains James Bannerman's The Church of Christ. While you may find the two-volume Banner of Truth version on the used book market, it is currently only available in a paperback version published by Westminster Discount Books and you can buy it at Westminster Seminary Bookstore.]