John Kennedy did not initially play much of a role in the wider affairs of the Free Church. Although ordained early in 1844 and attending the General Assembly as a commissioner about once every three years, he took no prominent role in Assembly proceedings until the 1870s. He did not deliver his maiden speech to the Assembly until 1872, when he was fifty-two. As one of his biographers wrote:

In the latter years of his ministry, he began to contribute significantly to the internal debates of the Free Church, first by the publication of a substantial theological work, relevant to broader contemporary discussions, in 1869, and thereafter through a steady flow of controversial pamphlets from 1870 onwards, through addressing public meetings, and increasingly through contributions in church courts, including the Assembly.

By these means, he helped to mobilise the majority of Highland evangelical opinion on his own side in the central controversy of the nineteenth-century Free Church, which concerned the constitution of the Free Church of Scotland, and its consequent relation to the other major Presbyterian denominations in Scotland – the Established Church and the United Presbyterian Church. This controversy commenced in the mid-1860s over proposals for a full incorporating union with the United Presbyterian Church, which were successfully resisted by a minority within the Free Church, Kennedy included, on the grounds of theological divergence between the churches over the doctrine of the atonement and especially over the Establishment Principle. For taking this ground the minority became known as the constitutionalist party. Following this setback, the controversy continued in a new form, as the majority party sought to vitiate the latter ground of separation by challenging the privileged position of the Established Church in Scotland, leading eventually to the controversial majority decision of the Free Church General Assembly to call for full disestablishment in Scotland. This call was strenuously resisted and opposed by a minority within the Free Church, located chiefly in the Highlands, and led by Kennedy and his friend, James Begg.