It's strange when our heroes are murderers. In this case, we feel Miss Emily's tragedy so acutely that we hardly feel the tragedy of her murdered lover.
Could we possible insert any of the other characters into the role of protagonist? Tobe would qualify, in terms of being a good guy, but his role in the story is minimized, so we can't use him. Besides, this story is all about Miss Emily and we're stuck with her as a protagonist whether we like it or not.