Clearly, both morality and ethics exist independently of holy books. Ethics are universals, and exist in every society, including ones that have no writing at all. All societies recognize that killing, stealing, lying, and screwing around simply lead to a society not working as well and more people suffering. That is an example of universal ethics.
Morality includes ethics, but also includes social codes particular to each society. For example, all societies have some form of dress code (though it may be as small as a string), and distinguish naked (in private) from dressed (in public). But the well-dressed aboriginal woman (topless) may be considered naked at the NY Opera House.
There are also many great works of philosophy, such as Plato and Aristotle, that are all about ethics and morals and are not holy books, but clearly seen as works of human thought.
The point you make about commentary that indicate what parts of holy books are to be followed arises, accordiing to some, because our sense of morality is changing. Punishments such as "an eye for an eye" and "a life for a life" and blood price (standard payment for accidental death) were moral positions when these books were written, and we look at them differently now. So universal ethics from holy books remain true, while social morals present in holy books may no longer be seen as valid. Depending on one's religious views, they are either set aside or re-interpreted.