The central themes of Peace Shall Destroy Many revolve around the concept of peace and the paradoxical possibility that peace may destroy, precisely as Wiebe's title indicates.
Central the plot and the themes is World War II. The protagonist, Thom Wiens, is driven to question the moral and political position of his pacifist Mennonite community when he sees that the farming community is making a profit out of supplying food to soldiers who are fighting in a war that the Mennonites denounce as being the destroyer of peace, which is seen as the higher, holier value (although the biblical foundation for that position is tenuous).
Another idea that is central to the plot and the themes is domestic disturbance and even violence amongst the Mennonite community itself. The community authority figure, Deacon Peter Block, rules with the kind of iron-grip authority that fascist rulers have, those against whom World War II is being fought.
A related idea and central theme, one that is foundational to how peace destroys many, is that the evil within the individual, in the heart of the individual, disrupts peace regardless of separation or retreat away from the peaceless chaos of the world outside a safe harbor, whether that be a safe harbor of the Mennonite community, home or individual beliefs.
Thom Wiens is forced to understand where true peace lies: Does peace lie in the iron-handed unthinking peace that comes from an order and system imposed from without or does peace lie in pursuing an undiluted, uninterpreted understanding of the Bible and of Jesus' teachings. Thom chooses to step away from the destructive order and system imposed upon him and the community from without and step into his own reading and understanding of the Bible to a liberating and internal peace.
Wiebe shows that, painfully ironically, peace--whether world peace, community peace, domestic peace or individual peace--often comes only after a destructive force shows the path to true peace and that, equally painfully ironically, there is no one agreed upon meaning of peace that all accept: The despot sees peace as blind following of his order and system, the religious community sees peace as (ofttimes blindly) following religious doctrines, the family sees peace similarly to a leader with a system and order being followed, the individual sees peace as that which gives inner tranquility, purpose and harmony. Equally ironically, all these views are highly subjective values and all may be flawed and in error. What must peace include to be true peace?