I believe that there are a few different things that we need to consider as we think about unity, subscription, and issues centered on church unity vs. purity (if you want to say that they are opposing thoughts).
1. What churches are available locally? There may be a perfect church on paper, but if there are not people locally with whom to fellowship, than you are a being pure in theory, but practice will have to be different. You will either have your papers with the pure church and fellowship with the erroneous church; or you will have your paper in the pure church and have false fellowship- emails, blogs, internet forums. This forsakes the face-to-face nature of the church.
The bottom line is that those who seek out the purest church for the sake of having their Confession usually end up being sectarian. What was Calvin's advice in letters to those who only had Lutheran churches to attend? Be Lutheran.
2. When a couple of ministers leave a denomination to be a pure church they are abandoning the duty to be reformers and those who answer the gainsayer. Time after time, in church history we see people abandoning the church to make something pure- that leaves the larger body with less sound men to fight against error.
Hence the couple of ministers that left have done damage to the body of Christ. It would be like if you had cancer and all of your antibodies left you because they did not like the cancer being there- you die. This is the problem with everyone and their brother starting presbyterian churches with 2-5 ministers: it NEVER ends, and the body of Christ is in further schism.
I could see if all of the church courts had been appealed to and the church refused to repent and kicked a man or group of ministers out- but to leave and start something because you have a problem with a secondary issue- that is schism and sin. (Of course, the main concern should always be for restoration with the sinning body.)
I am not sure of all of the ins and outs of Scottish church history and am in no position to judge all of the bodies (Church of Scotland, Free Church, Free Church Continuing, Reformed Presbyterians, Free Presbyterians, Associate Presbyterians, Associated Presbyterians, and many, many more) , but I feel confident in saying that this is not what Jesus Christ had in mind- and neither is a couple of 'pure' ministers who separate themselves from the body of Christ claiming to be the truest church or the purest church.
What was the Reformer and Puritan position on reformation and church unity?
You stay and fight for the sake of Christ until the established church will no longer have you. Were there faulty confessions in the Church of England before the Act of Uniformity? You bet ya! But our forefathers knew enough to set aside party spirit and to fight for the sake of the Gospel and Christ. We have a practical result of THIS practice of 'unity and purity' in the Westminster Standards.
If the Puritans had all left their churches to go start their own churches, I can say with a good conscience that the Westminster Standards would have never been written. There would be hundreds of smaller works that defined little 3-5 ministerial bands. The Westminster Standards are the practical outworking of a Reformed ecumenical spirit. There is no way to argue against this given the historical evidence.
This is my position, following in the Reformation and Puritan tradition. I will stay where I am and be a witness. A witness for the sake of the Gospel. A witness against what I see as error. A witness for the healing of a body that has been called to be one. I believe where I am is a good place with a lot of work being done for the Gospel.
I will never leave because of minor disputes or cultural baggage. I will not partake in schism.
There is a term amongst youth counter-culture that is helpful. It is called 'chasing the red dragon' and what it means is that you are looking for something that is not there and you will waste your whole life looking for.
I will not chase the red dragon of the purest church in the world- our Confession of Faith, chapter 25, says that even the purest churches under heaven are subject to both mixture and error.
I believe that we are confessionally bound to acknowledge this and to have the same faith of our Puritan forefathers- stay and fight under the captain of our souls, who loved a spotted and unfaithful bride enough to die for her.
I will live for her and pray that she can be pure in doctrine, practice, and single mindedness.
Two a'Brakel quotes to ponder:
It is not sufficient to merely join the church, to remain with her for some time, and thereafter to separate from her. One ought never to break away from and leave her under the pretense that the church is degenerate, in order to establish a pure church, for: First, the Lord has never blessed such endeavors. There have always been those (in the first church, both prior to her oppression by the antichrist as well as since the time of the Reformation) who under this pretense have broken away from the church. The Lord, however, has always overturned such endeavors, and such undertakings have collapsed of themselves when the initial instigators died. Due to a just judgment of God, however, such individuals have rarely perceived their errors and made confession of them, and have rarely rejoined the church. Rather, having been given over to their own stubbornness, they have remained independent as people without any religion, or they have succumbed to heresy and have joined themselves to such assemblies which most fully agreed with their errors. Such was the case with the Brethren in Hungary, and in our days the Labadists have arisen who have boasted of great things (II: 60).