MacKinnon is noted for his contributions to philosophical theology. He is particularly noted for the depth of analysis he applied to intractable theological problems, not least the refusal to simplify difficult questions in order to produce tidy or conclusive answers. His insistence on truth over tidiness is evident in his method of thought, an approach which some have labelled "open-textured". The label derives from MacKinnon's use of literary, artistic, and political sources in his work – modes of enquiry which operate in contrast to the systematic and epistemologically narrow approach of some theology and philosophy. The intensity of MacKinnon's thought was matched by his lecturing style, which was marked by "his dangerously strong charisma, his ability to terrify adversaries". Some former students admit to "spending more time mimicking him than following his arguments about Kant or Hegel." At Aberdeen he was notorious among the students for talking to the ivy on the walls of King's College. Former students Dame Iris Murdoch, Philippa Foot, and Lord Williams of Oystermouth expressed deep indebtedness and admiration for his input into their intellectual development. His influential input into important and relatively widely read thinkers' work, such as Williams and Murdoch, would suggest that MacKinnon's contribution to theology and philosophy is most strongly felt through the subsequent work of his students. By contrast, MacKinnon did not publish extensively, and that which he did publish is largely in short essay form and out of print.
MacKinnon often used a broadly Kantian metaphysics to determine the limits of a person's knowledge of God. Subsequently, there is a close relationship between God and ethics in MacKinnon’s work. But MacKinnon veers away from concluding that Kant collapsed God into ethics. Nor does he accept – the further conclusion that sometimes follows this – that Kant's epistemology precludes metaphysical realism, i.e. necessitates anti-realism, in ethics and theology. In The Problem of Metaphysics MacKinnon develops a Kantian epistemology and comes close to an agnostic position on God, except for the proviso that ethical decision-making has the capacity to make agents aware of a kind of metaphysical realism. He goes on to argue that it is in keeping with a Kantian metaphysics to deduce God from this sense of awareness: "Kant in the end a theist. ... His God does not enter into the texture of his exposition. ... he lies altogether beyond the frontiers of intelligible referential and descriptive statement. we are all the time thrust outside those frontiers, precipitated beyond them by a moral experience on whose formal unity, in the most diverse human situations, Kant insists." MacKinnon is, in this respect, against interpreters of Kant who consider his epistemology to have anti-realist conclusions. He is also quite specifically against the view that an anti-realist theology needs to be developed as renewed approach to Christian thought, e.g. the approach developed by Don Cupitt. Tragedy, construed as an ethical construct, plays an important part in the awareness of metaphysical realism. MacKinnon illustrates this with examples of tragedy from Shakespeare, Greek thought, and Jesus' parables, and concludes that "t is as if we are constrained in pondering the extremities of human life to acknowledge the transcendent as the only alternative to the kind of trivialisation which would empty of significance the sorts of experience with which we have been concerned".
Selected works
A Study in Ethical Theory
The Resurrection: A Dialogue with Geoffrey Lampe and William Purcell