In response to your first question, there is a pretty significant discussion in contemporary ethical theory regarding the concepts of obligation and duty. Elizabeth Anscombe, in “Modern Moral Philosophy” suggests that talk of duty is meaningless absent the existence of a lawgiver. Both Michael Stocker (“The Schizophrenia of Modern Ethical Theories”) and Bernard Williams (“Persons, Character, and Morality”) take this concern further, and argue that concepts of duty and obligation can be psychologically damaging to agents. While these authors don’t explicitly discuss the moralistic judgments and punishments your question cites, they do address your more fundamental concern that appealing to “duty” is problematic.
Your second question is harder to answer. Some might justify appeal to moralistic language and punishments on the grounds that they can be effective modes of getting people to do the “right” thing (even if they psychologically damage people in the process!). One might try to justify the workings of guilt and shame by appealing to aspects of human nature that make it the case that we feel guilty when we harm other people, and so on. This sort of justification could be quite plausible, so long as the feelings of guilt and shame are tracking something real (i.e., inherent to human nature), and not just some “doctrine” that people have been brought up to believe in.