The pig debate speaks to the huge character shift Bones went through over the seasons. In the season 1 episode "The Woman in the Car," Bones specifically says that she has feelings, but puts them aside in her work. Season 5 Bones is much more Vulcan-like, often acting as though she is only motivated by pure reason. Season 1 Bones suppresses her feelings so that they don't affect her work; season 5 Bones acts like she has no feelings to suppress.
And yet, a season earlier, Bones bonds so strongly with an animal that she is willing to adopt it. In "The Finger in the Nest," Bones wants to adopt a dog that was used to kill someone. But the dog has to be put down, as killer animals aren't generally allowed to live. Bones insists on a dog funeral, where she eulogizes the animal, saying, "Like all dogs, Ripley only saw the good in people. Dogs are like that. People should take a lesson." The Bones who mourns Ripley feels very different than the Bones who's indifferent to pig suffering.
