One of the reasons the nature/grace distinction is significant is because of its political implications. These are not always apparent, but they are real. As mentioned in a previous post, they have been used by some Roman Catholic traditions of thought to justify a kind of world empire centered in the Vatican, and others to justify complete pacifism.
In fact, it is possible to make an argument for pacifism based both on a “grace perfects nature” scheme, and on a “grace changes nature” scheme. In the case of the latter, the logic is obvious: grace changes humanity into a different kind of creature, such that different ethical laws apply to it, and one of these laws is the absolute prohibition of lethal force.
In the case of the former, the grace perfects nature view, the argument for pacifism was actually given in John Howard Yoder’s booklet, The Christian Witness to the State. While I don’t have the book in front of me, and am therefore writing from memory, I believe that towards the end of the book Yoder argues in the following way: in the Garden of Eden there were only relations of peaceful love. Thus, if God’s intentions inscribed in our nature from our created origin (i.e., natural law) are to be our guide for morality, we would have to conclude that pacifism is mandated by natural law.
Of course, there is a response to both of these arguments from a just war theory perspective. Against the view that grace changes nature, are firstly all the biblical texts which describe salvation as a restoration of some kind. Here would fit all descriptions of God’s work as “healing”, “rescuing”, “returning to life”, “reconciling”, and others. Secondly, there are actually no descriptions of salvation which imply that salvation is a transformation of our original nature. Mortality is swallowed up by immortality, but death is explicitly said to be the result of sin. Glory is given to us, but we originally possessed a glory in Adam that we have fallen short of. In Adam, humanity was prophet, priest, and king, and thus being promoted to these states in the eschaton does not imply a transformation of our nature either. Even the Spirit of God was breathed into us in the beginning, and so its dwelling in us at the End is no change beyond what we originally had the potential for. Now, we will no doubt possess all these things to a greater degree in the Consummation, but that only proves that our natural potencies were only partially actualized in the beginning, awaiting a more complete actualization in the future (even apart from sin). So there is no reason to deny that grace perfects nature, and positive reason to think that the relation of the two terms exists in this manner. This means pacifism cannot be grounded on this view, if it can be grounded at all, since there is no reason to believe such an externally added and extrinsic donum superadditum exists or ever will exist.
Regarding the second argument, that pacifism is required by the perfection of our nature, this overlooks the significance of the presence of sin in our world. That is, even if an individual had a perfected nature, the presence of sin in other people might require a kind of relation that would never be demanded in an unfallen protological state. That this is the judgment of scripture is fairly easy to demontstrate. Yoder’s point about the garden is correct: there would never need to be violence in an unfallen world. But it also proves something else: in an unfallen world, there would never need to be emotionally painful moral correction, nor shunning of any kind. But in the inauguration of the New Creation begun in Christ, the Lord taught his disciples (Matt 18) to exclude those who were unwilling to submit to the discipline of the community (and the earliest disciples understood this in a fashion that makes clear he commanded them to exclude people, which would never happen in an unfallen wrold: 1 Cor 5:2, Titus 3:10, 2 John 10-11, 2 Tim 3:5, Rom 16:17). This, of course, fits with the general principle that natural law requires us to do what is good, and that doing the good requires prudence. And prudence, inevitably, must weigh consequences. Because of sin’s presence in this world, sometimes lesser goods (like being sociable with people) must be outweighed by greater goods (like protecting physically and spiritually vulnerable people, including oneself in some cases, from dangerous individuals). Even the grace and power of God does not eliminate the tragic necessity for performing these acts, precisely because he wishes us to do these things; he does not give us the power to transform the hearts of evil people, but he does give us the power to avoid them and to protect others from their influence.