What mechanism is in place to protect and build up the unity of the visible church if congregationalism is accepted? False teaching destroys unity, but the mechanism for dealing with false teaching under congregational ecclesiology is left to the congregation itself. Particular congregations need the protection of other congregations, just as pastors need the protection and (sometimes) discipline of other pastors. It's good that my congregation can appeal to my presbytery if my teaching becomes suspect and the elders and I refuse to see my problem. That other elders can have authority over matters of doctrine in our church is our strength, not a weakness—for they may provide a more objective assessment of the problem in question (Prov. 11:14).Read the entire article HERE.
Moreover, in many congregational churches it's entirely possible for the Calvinistic minister to leave, only to be replaced by an Arminian one. Presbyterians have mechanisms for preventing such a drastic shift. I've learned a lot from my congregational friend Hunter Powell (the leading scholar of Puritan ecclesiology today), such as how much the Congregationalists needed the state to regulate true religion in the hope of achieving ecclesiastical unity. With today's separation of church and state, however, congregationalists have no such recourse for establishing wider church unity. And so one of the flaws of congregational ecclesiology is its crass independency and inability to regulate true religion on wide scale. Presbyterianism has a better mechanism in place to deal with false religion and establish true religion (such as the Westminster Confession of Faith).
Guy Waters observes, "Presbyterianism is essential to the well-being (bene esse) but not to the essence (esse) of the church. Non-acceptance of Presbyterianism is, therefore, no barrier to receiving a non-Presbyterian person as a Christian, or a non-Presbyterian church as a true branch of the church, provided that he in fact holds fast the only Head of the church, Jesus Christ." Thus, in the PCA we welcome any who are Christians as a regular member in our church, even if they are an anti-paedobaptist. If someone belongs to Christ we have no grounds for barring him or her from visible communion in Christ's body. Our desire for unity—objectified in our terms for membership—is our glory and Christ's glory (John 17:20-22), and this glory is best realized in the form of government known as Presbyterianism.