There are historical arguments on both sides.
The Coalition powers after the Napoleonic wars at the Congress of Vienna gave France a fairly soft peace in 1815 which proved very durable. Our own Civil War ended in the total destruction of the Confederacy and our nation saw the end of domestic warfare. Rome destroyed Carthage at the end of the Third Punic War, and went on to found a vast empire. The English and the Dutch in the mid Seventeenth Century fought a series of naval wars which were resolved in moderate peace terms which have lasted for centuries.
Sometimes generosity to a defeated enemy is a wise policy, sometimes it is not. There are too many other factors that enter into the equation for a general rule to be enunciated. One thing however is certain. Once a nation is in a war, if it does not win it, the nature of the following peace will be up to its adversary and not to it.
I would also note that if one takes a look just at Afghanistan, you can see a pretty good example where the United States established generous peace terms with the defeated enemy. While there is still an insurgency, it is pretty universally recognized to be more of a function of our broader problems with Pakistan (where the Taliban originated to begin with) and al-Qaeda than as an indigenous phenomenon. Not that this is of any great comfort to the Afghans living in border provinces like Helmand.
At any rate, I agree with the Don that these things are best sorted out on a case-by-case basis. I also think that there is the nature of the conflict to be considered. One of the bigger problems of the last half century has been that desire to wage overly humane wars has trumped these considerations when engaging in strategic planning - a perfect example of this would be what happened in Somalia in 1991, I think, where humanitarianism trumped the need to provide the necessary minimum amount of force needed to maintain security for the whole operation. I actually think that the standard of using the necessary amount of force needed to prevail in a conflict is quite in keeping with the classical understanding of Catholic teaching on Just War Doctrine that you use the necessary amount of force needed.
I also think that John J. Reilly places the discussion of ius bello in its proper perspective when he writes:
Governments normally provide disaster relief and social services, but then so do private agencies. The defining power of government has usually been a monopoly on the legitimate use of force, particularly of military force. The sections dealing with war, 2306-2316, rather grudgingly allow to states a right of self-defense, "as long as the danger of war persists and there is no international authority with the necessary competence and power" to maintain world peace. Presumably, then, a universal government would have as one of its functions the duty to police the world, though the principle of subsidiarity would suggest that local disorders should normally be dealt with by local forces.
The verb "police" here is precisely the right one to describe the Catechism's view of the role of the military. Sections 2306-2316 (which together comprise a division entitled "Safeguarding Peace") simply restate traditional Catholic doctrine on war. Peace is defined as not just the absence of conflict, but as the tranquility which naturally arises from a just social order. The familiar criteria for a "just war" are set out. Anyone who reads this material out of context is likely to be struck by its legalism. For statesmen in most places at most times, questions of war and peace are questions of policy, of contingency. While not quite lawless, perhaps no decision about going to war has ever been governed entirely by a legal formula. If the principles enunciated in "Safeguarding the Peace" are supposed to be normative, they are not descriptive norms.
What Catholic military doctrine does resemble is the criteria that well-run civilian police forces articulate regarding the use of deadly force. As the nightly television news will tell you, rules of this sort often work imperfectly. However, they do make sense for any law-governed society in which the authorities, too, can be held responsible for their actions.
In other words, Catholic doctrine best fits a world in which subsidiarity has already reached its logical conclusion. It assumes that a universal "law" and "government" are somehow normative. The present society of nations, in which states must resort to self-help to protect themselves, is provisional. Catholic doctrine looks toward a future situation in which there is some supernational entity with the acknowledged right to settle disputes among states, and the physical ability to make its decisions effective. In that world, the rigid legalism which the Catechism prescribes for questions of war and peace would be not only workable, but morally unavoidable.
This seems to be quite sensible to me, especially if you read the rest of Reilly's work and understand that he means something quite different from the current impotency of the UN when he talks about the issue of world government. He has a rather large body of work on this topic including several books that I think make a compelling case, at least to me. But regardless of whether you agree with him on world government or not, I think that if you understand ius bello as being similar to how police rules of deadly force work, it makes it possible to appreciate the subject without lapsing into the extremes of alarmism and hyperbole.