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Important practical compromises were made in the interests of domestic peace. The bishops, who after all were not the means by which reformation had arrived, were not allowed to say Mass but they were not compelled to subscribe to the confession of faith either, and neither was anyone else. Some of the bishops joined in the promotion of reform and their efforts were supplemented rather than supplanted by superintendents, appointed to direct the pastoral effort in areas without a sympathetic bishop. These new offices were not really rivals to the episcopal office, therefore, but a means of strengthening its pastoral role where that was perceived to be weak.23 Since the monarch was a devoted Catholic she could not oversee the Reformation in Scotland and as a result a General Assembly was formed modelled on the composition of the Scottish parliament.24 The role of the parish was perpetuated in the kirk sessions, later claimed on dubious authority to have grown out of voluntary Protestant congregations – privy kirks – operating prior to 1560. This version of the history of the Reformation emphasized again the roots of the Reformation among the flock, rather than its debt to the head. If their significance to the origins of the Reformation has been exaggerated or distorted, however, they were certainly of crucial significance to the subsequent development of Scottish Protestantism. Through the sessions the parish remained the fundamental unit of church organization, providing preaching, sacraments and discipline of the flock. It was these institutions which, over time, became the motor of Scottish reformation.25 Finally, weekly exercises took root, meetings where preaching could reach an audience beyond the parish, or reach parishioners not well served with a preaching ministry at home.26 In all, this was a hybrid and pragmatic solution, which supplemented the ancient institutions of the church by giving some of its functions to new bodies, and it developed over time in an organic way.

A second ambiguity, or compromise, was that the legislation setting up these new arrangements was not ratified. When Queen Mary returned from France in August 1561 she issued a proclamation enjoining obedience to ‘public and universally standing practices’ then current. While this did allow for the prosecution of ‘mass mongers’ it did not validate or endow the new church. Only after 1567, when Mary was deposed in favour of her infant son, James VI, was legislation counter to the Reformation rescinded. The provisional nature of the arrangements of the 1560s is also reflected in the fact that in 1573, when the position of Protestantism was clearly established, it was suggested that the General Assembly had served its purpose and the stewardship of the church might now return to the crown.27 It was certainly not the case that the General Assembly was by law the supreme authority in ecclesiastical matters. The founding vision of reformation in Scotland had not given the kirk a clear constitution or an unambiguous relationship to civil authority.

Over the following years there was growing pressure to adopt a Presbyterian model of church government in order to promote reformation, but this met with monarchical resistance. The institutions of the reformed church had been set alongside those of the old church, supplementing rather than supplanting them in order to promote the pastoral work of the reformers. The priority was the promotion of a pastoral ministry – supporting the preaching of the Word, true sacramental worship and discipline. As time passed, however, the institutional compromises of the 1560s came increasingly to be seen as presenting obstacles to that. Old church institutions were deprived of their pastoral role but not of their endowments, whereas the new institutions were given pastoral functions but inadequate endowments.28 Evangelists pushing for the establishment of a more active ministry might easily identify kirk sessions, weekly exercises,