When I talk about guilt and innocence as a major theme in Prisoner of Azkaban, I’m not just talking about Sirius Black. Even the subplots revolve around similar ideas. In these chapters, Ron feuds with Hermione when he believes her cat has eaten his rat, while Hagrid goes to defend Buckbeak the hippogriff in court.
Crookshanks did not eat Scabbers, although it certainly looks that way now. In fact, Ron is right that Hermione’s cat has an obsession with attacking his pet rat, but it’s not because he wants to eat him. He’s smart enough to know an animagus when he sees one and is attempting to help Sirius by bringing Peter Pettigrew to him. Not that the first-time reader is aware of that at this point in the story. However, as Hagrid points out, even if Crookshanks did eat Scabbers, he’s behaving as all cats do, and Hermione is guilty only of failing to prevent that. How guilty does that make her? Well, it depends who you ask. Hermione herself would say not at all, while Ron would say it makes her very, very guilty.
Then there’s Buckbeak. It’s true that he did attack Malfoy, but only because Malfoy provoked him. He’s really no more dangerous than any other hippogriff. However, should such easily-provoked creatures really have been introduced in the very first Care of Magical Creatures lesson? Does that make Hagrid guilty for having them work with an animal they weren’t prepared for? Should anyone, human or animal, pay the price for Malfoy doing exactly what they were told not to? That’s an even harder question to answer. Hagrid doesn’t always make wise decisions about what kinds of animals are appropriate for young kids to be around, but he had no way of controlling Malfoy’s reckless behavior.
What I’m getting at here is that guilt isn’t always black-and-white. This is hardly the first time that’s been brought up. In the previous book, for instance, Hagrid is framed for opening the Chamber of Secrets but still guilty of keeping a monster in the castle, while Ginny did open the Chamber and set the basilisk loose, but only because she was possessed by Voldemort. But it’s especially important in Prisoner of Azkaban, because it’s all setting the stage for the twist ending.
Speaking of the twist ending, here’s another big sign that Sirius is innocent: when he sneaks into Gryffindor Tower, Ron wakes up to find him standing over his bed, holding a knife. They all wonder why he simply vanishes rather than continuing to search for Harry, and they assume it’s because there are so many people around. However, it makes a lot more sense if he was never after Harry in the first place.