I would argue that the main theme of the story is the effect that war has upon ordinary people. A casual glance at a history book might give us the impression that war is all about epic battles, glory, and acts of heroism. But there's another side to war, a much darker side in which the lives of innocent civilians are disrupted and destroyed. It is this side of war that is the main focus of Across Five Aprils.
In keeping with the book's perspective, we're never given any detailed firsthand descriptions of battle. Instead, the Civil War takes place at some distance from the Creightons and their neighbors, yet it still touches them deeply. Even in this quiet, remote corner of rural Illinois, it's impossible to escape the often horrific consequences of war.
On the home front, war undermines communities, turning people who had previously lived peaceably together against each other. Some members of the local community have got it into their heads that Jethro's brother Bill has joined up to fight for the Confederates. This wholly unfounded rumor makes the Creightons the object of suspicion. Some of their neighbors show their displeasure at what they perceive as the Creightons' treachery by setting their barn on fire. The message conveyed by this unpleasant episode is clear: though war can often inspire ordinary people to do extraordinary things, it can also incite basically decent people to do things they would never normally do.