At no point in the proceedings does Elly ever stop to consider anything from the dog's point of view. Good ol'Farley will never understand English on the same level you and I can but he has learned to associate the sound of the word "bath" with being shoved into water and having his scent scrubbed off of him. While he does know that for some reason that couldn't possibly make sense to him, the humans like the unpleasant smell he has after he gets dunked into the scary tub full of scary water, he doesn't especially care because he wants to smell 'right' and immediately treats himself to a satisfying roll in the dust to get rid of that awful stench the people like. Why it is that he isn't allowed to smell the way he wants to is something that he isn't able to understand.
He shares this inability to understand the world around him with Elly. She can read books about animal behaviour, she can be told how dogs will act, she can watch dog trainers on television but she refuses to accept their advice because she doesn't think that his never being able to think like a person is especially fair. Just as the point of the Mystery Virus arc is all about how horrible it was that Elly had to take care of a sick kid, all the shrieking she does at Farley is all about how terrible it is that she has to change how she behaves because a dog won't.