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The following is an excerpt from The MacArthur New Testament Commentary on 2 Corinthians 6.
Believers and unbelievers inhabit two opposing worlds. Christians are in Christ’s kingdom, which is characterized by righteousness, light, and eternal life. Unbelievers are in Satan’s kingdom, characterized by lawlessness, darkness, and spiritual death. The saved and the unsaved have different affections, beliefs, principles, motives, goals, attitudes, and hopes. In short, they view life from opposing perspectives.
Consequently, relationships between believers and unbelievers are at best limited to the temporal and external. They may enjoy family ties, work at the same job, share in business relationships, live in the same community, experience the same hobbies and pastimes, and even agree on certain political and social issues. But on the spiritual level, believers and unbelievers live in two completely different worlds.
The Corinthians had struggled greatly to make a clean break from the idolatrous and immoral lifestyle of their past. Despite having professed faith in Christ and become part of the church, some in the congregation were still clinging to elements of their pagan religion. And though they, like the Thessalonians, had “turned to God from idols to serve a living and true God” (1 Thess. 1:9), still they failed to make a clean break with their idolatrous past. The lure of their former paganism, which permeated every aspect of life in Corinth, had proven hard to shake, as Paul’s first epistle to them makes evident.
Making matters worse, the false teachers who had come to the church brought with them a quasi-Christian syncretism of gospel truth, Jewish legalism, and pagan mysticism. They were eager to stay connected to the Corinthians’ former behavior, to make themselves more popular and, thereby, more prosperous. Thus Paul gave this mandate to separate.
The familiar command to separate in this passage is frequently both misunderstood and violated. The separation demanded here does not refer to refusing association with those who do not follow a certain set of rules for living the Christian life, as many legalistic Christians have advocated. It does not mean refusing to cooperate with those who teach the truth but do not agree with all the distinctives of one’s own theology or ministry style. Nor does separation mean retreating completely from the world into monasticism. And separating from unbelievers does not, as some at Corinth imagined, mean divorcing an unbelieving spouse (1 Cor. 7:12–13). Biblical separation certainly does not cancel the church’s responsibility to “go into all the world and preach the gospel to all creation” (Mark 16:15).
So what did the Holy Spirit intend by His command not to be bound together with unbelievers? Bound together translates a participial form of the verb heterozugeo, which means, “to be unequally yoked.” Paul drew his analogy from Deuteronomy 22:10, where the Mosaic Law commanded the Israelites, “You shall not plow with an ox and a donkey together.” Those two animals do not have the same nature, gait, or strength. Therefore it would be impossible for such a mismatched pair to plow together effectively. Nothing in the context would lead to the idea that he is referring to earthly issues of human endeavors. In Paul’s analogy, believers and unbelievers are two different breeds and cannot work together in the spiritual realm. He called for separation in matters of the work of God, since such cooperation for spiritual benefit is impossible. The false teachers were eager to blend the people of God with the pagan worshipers, because that hinders the gospel. That is what this text forbids.