Hondo is a story about loyalty and integrity. Many of the central themes in the narrative have to do with fairness between people groups, and Hondo's own mixed background allows him to exist on both sides of the conflict. His clarity makes him an excellent judge of character, so much of the story involves mercy and betrayal as well, as ways of talking about justice in conflicts like the Native American Wars.
Hondo doesn't ever have to abandon either side of the war, either, which is notable. When the army comes through, Vittoro and Hondo have an agreement in place to protect Hondo from having to pick sides. When Vittoro leads the battle against Hondo's cavalry, Hondo does nothing, but when the evil man, Silva, picks up the same pursuit, Hondo helps his old comrades to escape. This may seem like he changed sides, but he hasn't. By regarding each person independently, he is able to judge the motivations of each person, and then he intervenes when necessary.
Hondo's consistent willingness to offer trust and second chances, along with his notable mercies throughout the novel, are indicators that Hondo is a Christ character. He replaces the husband who he killed, which is a Messianic idea as well, the merciful arbitrator. Interestingly, when Hondo is offered the chance to kill someone whom he has just causes to kill, he doesn't hesitate, and he always pulls the trigger first. This excellent ability to know justice makes him an example for navigating hopeless conflicts with a sense of poise, bravery, and chivalry.