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Submitting to men is the whole idea behind denominationalism. It is based upon the idea that the Church is an earthly organization, and that in order to "join the Church," one must join an organization, headed by men. It presumes that the Church is the organization, rather than the people (kahal, "congregation or assembly of people"). It presumes that faith in Christ is insufficient for one's justification.
For many centuries, this was the position of the Roman Catholic Church--and still is, officially, though many priests no longer believe this after studying the Scriptures on their own. Yet it is still the position of many Protestant (and other) denominations which consider their own organization to be "the True Church." All who teach this show themselves to be a part of Saul's government.
Needless to say, I disagree with that exclusivist doctrine. God sees clearly whether or not there is faith in any man's heart, and He determines who has a relationship with Him and who does not. One's relationship with God is not the same as one's relationship with denominational organizations. An organization, whether recognized by the IRS or not, can be a very useful servant, but it is a tyrant when it becomes the master. That is the essence of the matter.
Insofar as the prophetic office is concerned, let me give an illustration. Suppose we have a family who are members of an organization called the Church of Bethlehem. One of their young men begins to show potential as a prophet of God. Let us say that he truly is called as a prophet.
One day the pastor gets up and says to the people, "Our Church is old, and people just won't come here unless we build a $30 million dollar building to attract them. I have talked it over with the elders, and we are going to 'believe God' for a big new Church building."
Soon afterward, the word of the Lord comes to the prophet, who says, "Thus saith the Lord: Did I command you to build a $30 million building? Why do you want to attract those who are looking at the outside and who would come merely to be entertained? I did not tell you to do this. Do not put such a burden of debt upon your people to gain such poor quality believers."
The preacher, of course, was offended. If he could have heard such a word himself, God would have spoken it to him. But since he harbored an idol in his heart (a desire for a large and prestigious church), he could not hear such a word. So God raised up a prophet to give him this word.
The preacher's pride was pricked, and he felt like the prophet was undermining his authority. After all, HE was the one called of God to govern the people, and this prophet was clearly out of order. So the prophet was called before the elders, reprimanded for being "out of order," and told to repent and submit to God-ordained leadership.
At this point, the prophet was faced with the most important decision of his prophetic career. He could submit to the Church, or he could submit to Jesus Christ who gave him the word that the preacher could not hear.
The Church no longer kills its prophets by burning them at the stake. No, now they kill the Lord's prophets by turning them into Church prophets. They kill them by making them submit to men rather than God. If the prophet in our illustration agrees to submit to men, then men are his top gods. It is a matter of priority--who is the highest god? The top authority?
I believe that we should do all that we can to live peaceably with all men. There is nothing wrong with submitting to men, as long as it does not interfere with our submission to Jesus Christ FIRST. In fact, we are to submit to Christ in men, rather than to men themselves. This is the heart of the whole matter, and it is true for all. Submit to the word of God, regardless of who is giving voice to that word.
But in the case of a prophet, the damage done is in the fact that the Church prophet is limited in what he can hear from the Lord. He can hear only that which is acceptable to the Church leadership. This means that he cannot hear a word that goes beyond the hearing capability of the leadership.
And this goes against the very reason why God separated the prophetic office from the priesthood. God cut off the arm of the priesthood of Eli precisely because Eli refused to hear the word of the Lord to correct his corrupt sons and, if necessary, remove them from the priesthood. So God took away the prophetic office from him and raised up Samuel as the first of the prophets as such.
Prophets do not have to thunder maledictions or live in the desert to be true prophets. Some would-be prophets today seem to think that they have to be mean in order to prove their prophetic callings. Some seek to set up their own little cults and curse anyone who does not recognize them. But so often such "prophets" are motivated more by the spirit of envy and strife than by the love of God. They envy other Church leaders and simply set themselves up in competition with them for control over others. If they are successful, they end up establishing just another denominational manifestation of King Saul and Eli.
Thus, there are two extremes to avoid. The first problem is that the prophet submits to men rather than to God. The second problem is that the prophet is simply obnoxious and can't get along with anyone, because the love of God does not dwell in him.
Prophets do not have a license to be obnoxious. No matter whether one is an apostle, prophet, pastor, evangelist, or teacher, all leaders are manifested by their love--not merely their love for God, but also their love for mankind. The entire five-fold ministry mentioned in Eph. 4:11 was for the purpose of equipping the saints for the work of the ministry and building up the body of Christ.
If I may say something more personal here, I am a teacher. My teaching ought to equip the saints so that they can better minister according to their own callings. My teaching ought to build up the body of Christ, rather than to tear it down. The same can be said for all five callings listed above. Each calling is simply a different method of equipping and building. Paul said nothing here about the calling to turn the people into their servants. It was to train people to be better servants of God.
Having said this, however, history shows that true prophets and false pastors inevitably will come into conflict, because they have different goals. One is working to increase his own kingdom; the other is working to increase the Kingdom of God.
Likewise, true pastors and false prophets will also come into conflict, as will true apostles and false apostles (2 Cor. 11:13). It is often difficult to distinguish between the true and the false. The solution is NOT to leave such decisions to the leaders. The solution is for the leaders to train the people to discern for themselves.
It is the same with hearing God's voice, which is often difficult. The solution is NOT to leave it to the leaders. The solution is for the leaders to train the people to hear for themselves.
For this reason the five-fold ministry was ordained of God. It was to equip the saints and to build up the body of Christ--until such time as they have worked themselves out of a job and the five-fold ministry becomes irrelevant. As for myself, I look forward to the day when the provisions of the New Covenant are fully manifested, for then I will no longer have to teach my neighbor. He will already know God for himself, and my calling will be irrelevant. (See Hebrews 8:11.)