I have frequently been asked why we call our churches "Presbyterian." Sometimes when I explain the reason I get another question: "Do you all think that your system of church government is that important?" That's a fair question.
Thirty years ago I might have thought so, but not anymore. I remember being young and idealistic about the wonders of the presbyterian "system" of government. You know, checks and balances, limited authority, plurality of leadership at the local level, a series of graded courts, grass-roots (bottom-up) authority, connectionalism, biblical names for church leaders, etc.
Having experienced abuses of power in non-presbyterian churches, my friends and I were positively ecstatic about the Presbyterian system of government and ready to embrace it all as ecclesiastical uptopia. We actually thought that the form of government itself would prevent abuses. That there was something about doing ecclesiastical government right that guaranteed the peace and purity of the church. To say the least, we were a bit naive.
Perhaps these kinds of misplaced hopes are endemic to Americans. After all, some people actually believe that the U.S. is "a government of laws and not of men." In business we think that coming up with a new organizational flow chart is the way to fix problems.
But it's not true. Laws don't govern, people do. Systems don't administer justice and provide leadership, people do. A business or nation can be organized out the wazoo for efficiency and productivity yet still fail miserably because the wrong kind of people are leading the company. A nation can have the most just laws and the most reasonable form of government and yet without the right men to fill the positions of authority none of that really matters.
Systems of ecclesiastical government do not lead churches, men do. Rotten men in finely crafted, biblically-labeled positions of authority will muck it all up. If you have ever read John Buchan's Witchwood, you'll know what I am talking about. Here's a novel where Presbyterian government is used to persecute a righteous minister and run him out of his parish. It's a sober reminder of the kinds of abuses that can inhabit presbyterianism.
Of course, we need not look any further than the New Testament. In the Gospels, the OT church leaders, precisely organized and assembled in conformity to God's revelation, nevertheless condemned Jesus to death. The presbyterian form of government did not prevent the priests and elders from committing the most heinous act of injustice in human history.
That is why God is much more concerned with the character of men who lead the church than he is about the precise system of ecclesiastical government.
Back to the OT church in the Gospels. There were in fact important irregularities in the way the Jews were organized. The high priest was not from the divinely-sanctioned line of Aaron through Zadok. But Jesus in his condemnation of the rulers of the Jews (Matt. 23 for example) never picks at the organizational problems. Jesus never mentions what we might call a technical problem with the High Priest's appointment. Rather, he goes after the men themselves, their foul character and their bad behavior.
God is much more concerned with the character of men who lead the church than he is about the precise system of ecclesiastical government.