Christ's High-Priestly Prayer: Unity, Yes, but with Whom?

"I do not ask for these only, but also for those who will believe in Me through their word, that they may all be one, just as You, Father, are in Me, and I in You, that they also may be in Us, so that the world may believe that You have sent Me. The glory that You have given Me I have given to them, that they may be one even as We are one, I in them and You in Me, that they may become perfectly one, so that the world may know that You sent Me and loved them even as You loved Me."
- John 17:20-23

In this passage, part of what is commonly called Jesus's High-Priestly Prayer, the Redeemer asks His Father to bring unity among Christians. Thus, to desire unity among believers is a godly and biblical desire. But then practical questions begin: with whom am I to have unity? How am I to bring about biblical unity? The problem comes because this isn't the only passage relevant to the question of unity. 

In both Testaments, we can find repeated warnings that God expects His true people to be discerning regarding our allies. Leviticus 10:10, "You are to distinguish between the holy and the common, and between the unclean and the clean..." Leviticus 20:25-26, "You shall therefore separate the clean beast from the unclean, and the unclean bird from the clean. You shall not make yourselves detestable by beast or by bird or by anything with which the ground crawls, which I have set apart for you to hold unclean. You shall be holy to Me, for I the LORD am holy and have separated you from the peoples, that you should be Mine." Ezekiel 44:23 (speaking of the clergy), "They shall teach My people the difference between the holy and the common, and show them how to distinguish between the unclean and the clean." II Corinthians 6:17, "Therefore go out from their midst, and be separate from them, says the Lord, and touch no unclean thing; then I will welcome you..." James 4:4, "You adulterous people! Do you not know that friendship with the world is enmity with God? Therefore whoever wishes to be a friend of the world makes himself an enemy of God." Revelation 18:4, "Then I heard another voice from heaven saying, 'Come out of her, my people, lest you take part in her sins, lest you share in her plagues...'" This last verse is especially applicable to my purpose in writing this, because it explicitly commands separation from the false church. Here in my local area, the Rev. Robert Austell, of Good Shepherd Presbyterian Church (PCUSA), a self-described "conservative evangelical," declared his candidacy for moderator of their general assembly.
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In a presbyterian church, the moderator acts as chairman of the meeting, and the office is usually voted on at the beginning of the meeting, or annually, depending on the level of the court. In the election, Rev. Austell came in third of the four candidates. According to the article in our local newspaper, "while many congregations who share his theological views have left Presbyterian Church (USA), he and Good Shepherd are staying put. In a time of culture wars and deepening spiritual divides, Austell hopes to unite." 

The reporter is correct: many evangelical congregations have fled the PCUSA for more-conservative pastures, mainly in the PCA, but also the Evangelical Presbyterian Church and the Associate Reformed Presbyterian Church, not to mention the new breakaway group, the Covenant Order. In 1982, the then-United Presbyterian Church (which merged the next year with the Southern Presbyterian Church to form the current PCUSA), ordained Mansfield Kaseman to the ministry, though he denied during his examination both the deity of Christ and the resurrection of the body. The inerrancy of the Scriptures is almost-universally denied by PCUSA officers. In 1923, J. Gresham Machen, then a minister in the northern Presbyterian Church, in his book Christianity and Liberalism, demonstrated that liberalism is not a version or interpretation of Christianity, nor even related to Christianity, but is rather a completely different type of religion from Christianity. Yet, this is what Austell wants to be united with. 

I want to ask him this question: how does the unity you seek line up with the Scriptures (see above)? To my mind, that is the only legitimate standard of judgment. And again to my mind, Austell's desire fails to match that standard.