This episode focused mainly on the morality of others, what others have done and what they choose as their atonement for their past actions.
Similarly, the Doctor identifies with this because of his own past, the things he'd done and everything he's been trying to make right because of it. When he sees evidence of what Kahler-Jex had done, the horrendous acts he'd committed if only to save his people and to be labeled a war hero. If there's one thing that the Doctor does not tolerate is the willingness of torture to win a war. He does not do well with this kind of stuff. Of course, this episode we see him completely lose his sense of composure and just lash out. He yells angrily, and he basically forces Kahler-Jex to pay for his crimes. The scene between the Doctor and Amy is perhaps the best scene in the episode, because she practically tells him that this is not what they do, this is not what he does. When she says to him that he's been traveling alone for too long, it really hits hard because he knows it's true. We've seen this happen to him before. If he doesn't have some kind of steady ground, someone to call him out when he steps out of line, he'll spin out of control.
So in a sense, Amy and Isaac (who died heroically to protect his friend) were the voices of reason for the Doctor. Amy set him straight, and Isaac reminded the Doctor that they're good men, they just forget sometimes in the midst of everything.
Which is why, after this when he is appointed Marshal, he appoints Amy as his deputy. Because he trusts her to keep him grounded. That is, above all, their relationship in a nutshell. ♥
So yeah, this episode I liked a whole lot. It was, essentially, a morality tale.
Little things that I really enjoyed about the episode:
++ The mentioning of Amy being a mother. We all know this, but the show sometimes doesn't reference this enough, especially from the premiere when you'd think there would be some kind of mentioning of River Song being their daughter. But here, someone recognizes the signs of someone being a parent, of the warmth and love and sadness but ferocity. This is something I wish would be brought up more, because regardless of them not being able to have more children, Amy and Rory are still parents to River.
++ The boy horse who is named Susan and wants people to respect his life choices. Plus, the Doctor talking to him adorably. Bless. ♥
++ THE STETSON HAT. :D