The subject matter of a literary work is comprised of the characters and plot. Saying, for example, that the subject of Jane Austen is the marriages of the Bennett girls is merely describing what happens within the novel, but not making an moral judgement about the novel.
Morality consists of a sort of judgement made about the subject, sometimes made explicitly by the narrator, and sometimes by the reader. So, for example, one might say that the narrator of Pride and Prejudice thinks that marrying purely for money or trapping someone into marriage by lying is morally bad.
All stories have subjects. Not all have explicit morals.