The discussions of the historical positions are helpful. It would be useful to see any available evidence that the 1843 or 1900 Free Church of Scotland committed herself to a TR position. Absent that, evidence has been presented that the Free Church of 1843 did not understand her constitution to require acceptance of the TR.
I think, however, the fundamental issue is the doctrine of visible church unity. So, James Walker: "True Churches of Christ, side by side with one another, forming separate organizations, with separate governments, seemed to them [Rutherford, Durham et al.] utterly inadmissible."
The language of our older divines on the sins they allow in a church while union must be maintained is fairly extreme. Consider Rutherford from A Peaceable and Temperate Plea for Paul's Presbytery [text not modernised]:
"every false worship doth neither make a true Church, a false Church, or no Church; neither giveth it a ground and warrant of Separation; for there was much false worship in Corinth, where many were partakers of the Idols Table,
1 Cor. 8.
10. and many denyed the Resurrection, and so Thyatira, Pergamus,
Rev. 2. where were Balaams doctrine, and Jezabel the false Prophetesse, and yet none of these are to be separated from, as false Churches, and the Separatists would observe this, that when Churches in the New Testament are most sharply rebuked, if communion with these Churches going on in their sinnes be Idolatry and false worship, and offering of Devils Images to God, how is it, that the Lord and his Apostles rebuketh the faults, but never warneth the true and sound beleevers to separate and make a new Church?"
Or again:
"Paul doe not only not command separation in the Church of Corinth, but also command and approove their meeting together in Church-communion,
1 Cor. 5.
4.
1 Cor. 11.
18,
20,
21,
22.
1 Cor. 14.
23.
1 Cor. 16.
2. where there was schismes and contentious,
1 Cor. 1.
12,
13. envying and strife,
1 Cor. 3.
3. incest, and incest tolerated, such as is not named amongst the Gentiles,
1 Cor. 5.
1. going to law with their brethren for gain before Infidels,
1 Cor. 6. Harlotry, v. 15, 16. Eating at the Idols-Table,
1 Cor. 8. Keeping fellowship with Divels,
1 Cor. 10.
20,
2,
22. comming to the Lords Table drunken,
1 Cor. 11.
21. eating and drinking damnation, v. 29, 30. A denying of a fundamentall point of faith, the resurrection of the dead, and that with scoffing at it,
1 Cor. 15.
35. Murthering of weak soules, whom Christ had dyed for,
1 Cor. 8.
12,
13. Pauls name despitefully traduced,
2 Cor. 10.
8,
9. &c."
Walker notes, as he is commenting essentially on these and similar extracts from Rutherford, "Positions sufficiently startling were thus laid down by men whose whole life was nevertheless a battle for orthodoxy."
He also argues this is the constitutional view of the second reformation church: "The doctrine I have briefly explained was the doctrine eminently of the Confession period, - the doctrine of our Presbyterianism in the day of its power and its glory." Walker notes, however, the retrenchment of the church from this position: "it is clear to me that there is now a change of view or feeling. What used to be called the Separatist view... is making way [i.e. is now held]."
The key, for me, to remedy our divided state is the older doctrine of the church. Only in theologically engaging with what our older theologians would tolerate before division will current discussions around what justifies continued separation be set in proper proportion. I agree the principles of Rutherford are hard to apply in many circumstances - I believe, however, they can clearly be applied to the current Psalm singing churches of Scotland.