Looking at it with a purely scientific perspective, societies developing moral codes which included the prohibition of incest had an advantage over societies devloping moral codes which did not prohibit incest.
That's true, but societies then tended to either be religion-centric or amoral. That doesn't necessarily say anything about incest itself.
That's a false dichotomy; to the best of my knowledge of early peoples, their culture and moral codes varied significantly, and religion wasn't merely an outpouring of emotion and "spirituality." It was the basis for early regimentation and structure of society. And many early religions probably instilled many traits that are useful to a primitive society, such as a stronger work ethic, sense of cooperation, and goodwill towards others (and abstinence from incest). Societies that developed a moral code that encouraged members to excell in these traits would have had a strong advantage over others.