The story came up because of a astronomical event. The Aryans considered Orion (
Mrigashiras - Antelope's head) to represent Prajapati (the Supreme God), because prior to 4000 years, the sun rose in the constellation of Orion on the day of vernal equinox and that was considered the beginning of the year.
Now, due to precession of equinox, sun started slipping from Orion to Aldebaran, which represented his daughter, Rohini. Aryans thought Prajapati had incestous inclination towards his daughter, and that it foretold of a great calamity. So, the story of Rudra beheading Prajapati came about. That is the time when the worship of Prajapati (Brahma of the Puranas) was stopped. Later, Aryan priests moved their beginning of the year by one month and took rising of the sun on the day of vernal equinox in the asterism of '
Krittikas' (Pleiades) as the standard. Another change was done around 600 AD by the Indian astronomer Varahamihira. Then again, the standard was changed by one month on the rising of the sun on the day of vernal equinox in the asterism of '
Ashwinis' (Arietis).
We are astronomically already due for another change to '
Revati' (Piscium), but that would not be done for the reason that we now calibrate the year by Zodiac and not by Asterisms. I have not been able to find the exact reference in BG Tilaks books (in time, I will), but IMHO, this also will be helpful. This is quoted from his book "Orion or the Researches into the Antiquity of Vedas".