The Church affairs of Scotland were not settled in accordance with the desires of William. It was no secret that he wished to secure complete toleration for all dissenters. He was anxious to avoid all measures which could interfere with the projected Union of the Kingdoms; and it is probable that his hope was that some plan might be devised for establishing the same system of Church government throughout the whole island. When he received from the Government in Scotland the draft of the Act which it was proposed to pass for the establishment of Presbytery, he made a number of amendments which had a double purpose; to remove expressions which might raise doubts in England with regard to the Union, and to conciliate the Episcopalians in Scotland. For instance, it was stated in the draft that the Reformation in Scotland had been the work of Presbyters “without Prelacy.” This statement he deleted. In the draft, Presbytery was described as “the only government of Christ’s Church in this kingdom.” William was of opinion that a better expression would be “the government of the Church in this kingdom established by law.” The rest of his suggestions were of a similar character. Everything in the shape of an assertion that Presbytery was a better system than Episcopacy was carefully avoided, and the only reason given for establishing the former was, that it was more in accordance with the wishes of the Scottish people. At the same time he explained that it was his desire “that those who do not own and yield submission to the present Church government in Scotland shall have the like indulgence that the Presbyterians have in England.”
The Act was submitted to the Estates, and became law on the 7th of June 1690. It declared Presbytery to be “the only government of Christ’s Church within this kingdom”; it condoned the action of the peasantry in expelling the Episcopal clergy by force; and it placed the government of the Church in the hands of the sixty ministers who had been replaced in the livings from which they had been ejected at the Restoration. Yet the Government acted on tolerant principles. All Episcopal clergymen who took the oaths were left in peaceable possession of their churches, without being called on to submit to the Presbyterian Church courts; and some even of those who refused to take the oaths, and who prayed publicly for the late king and his family, continued to enjoy their livings without molestation.[107] After a few years, when it was seen that the Jacobites were quite irreconcilable, an Act was passed which provided that no one could hold a benefice without taking the oath of allegiance, signing the assurance, which was a declaration that William and Mary were the only lawful sovereigns of the realm, signing the Westminster Confession of Faith, and submitting to the Presbyterian system of Church government. Yet so lenient was the spirit of the Whigs that, instead of vigorously enforcing this law, they superseded it, to a great extent, by another and milder Act, under which taking the oaths to Government became the only qualification required from any Episcopal preacher in Scotland.