I think that the main point in the situation of O' Connor's story is to illuminate a condition of humanity during war.  It is a condition that in  which critic Patricia Robinson suggests O'Connor suggests that "in war, hatred and revenge drive out ethical and moral intelligence.’’  In a condition in which people are supposedly enlightened and endowed with the gift of rational thought, the point in O'Connor's story is to show that in war, humans do not necessarily embody such a lofty perch.  Rather, they become creatures that retreat into duty and other domains in order to evade the personal responsibilty and agonizingly brutal consequences that go with it.  

For majority of the story, the English captives and Irish captors seemed to get along quite well.  The animosity of war and the intensity of the conflict had been kept at bay while both soldiers recognize one another as soldiers and not partisans.  In the hue of such a condition, the Irish soliders and British soldiers refer to one another as "pals" and "chums."  Yet, when the order to execute the British soldiers becomes evident, the Irish soldiers do not take action in the name of friendship forged.  Rather, they retreat into the cave of duty to evade responsibility.  The main point of the story is to illustrate the lack of "ethical and moral intelligence" in war.  No cause is honorable enough to cause such primal elements of humanity to be abandoned so easily.  Noble objects to the mission, but does nothing about it.  He digs the holes in the ground for the bodies.  Bonaparte wishes that the English soldiers would escape, but he also does nothing to act on what he knows is right.  In the end, the bonds of tenderness and friendship are abdicated in the nebulous realm of duty.  Both Bonaparte and Noble do not feel honored in what they are to do, but both do it anyway.  It is this condition, illustrating how there is a lack of "ethical and moral intelligence" in war, that becomes the main point illustrated in O'Connor's story.

What is the central idea of "Guests of the Nation"?

The central idea of O'Connor's work is that "in war, hatred and revenge drive out ethical and moral intelligence.’’  This condition is brought out in the ending.  After befriending the British soldiers, the Irish soldiers are forced to adhere to a code of duty that seems to deny personal choice and voice. Bonaparte and Noble participate in "monstrous acts of evil" under the code and cover of duty.  

The central idea of the story is this aspect.  War brings out the worst in humanity.  It is not one in which there an be any clear winners.  The British soldiers lose because they are to be killed in the name of partisanship.  The Irish soldiers end up losing, as well, for their moral character cannot be cleaned of the stench attached to what they did.  It is for this reason that Noble falls to his knees in prayer at the end, almost begging forgiveness which he knows he will never receive.  Bonaparte becomes emotionally distant as a result of what he has done.  The central idea in this ending is that war generates a condition in which there is only loss and nothing in terms of "victory" is evident.