The submission we're talking about is submission to the corporate direction, not asking someone to violate their personal convictions. If someone over you in the Lord says, "Sit down" at a corporate gathering, you sit down. If they say, "Down this Jack Daniels," feel free to resist.
Submitting to a report regarding a doctrinal issue is by nature a matter of conscience. The color of the carpet or matters of order are a different story and I would agree with you.
I just believe there's a point where standing against a few thousand of your brothers and sisters in the Lord (including those in authority) reeks of self-importance, not pure convictions.
You would have to judge a person's heart to know that. By your statement any time a person stands in opposition to the majority and their leaders they would have to "reek of self importance." The Episcopal Bishops who stood in opposition to their leaderships ordination of homosexuals must have "reeked of self-importance." I guess Martin Luther, John Wesley, and every other reformer must have smelled to high heaven. It would seem easy to stand for your convictions if you only had to stand when you were in the majority. As the great theologian Groucho Marx once said, "These are my conviction. If you don't like them I have others."

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