I actually proposed that the scene at the waterfall has nothing to do with Earth - it is just 'A Planet' in deep space in the far distant future. Mankind has evolved into a superior species, taking over as the new galactic engineers, and starting the cycle all over again. This scene is actually taking place long, long after the events of Prometheus!
What you are witnessing is Earth2 (3, 4...?!), started by human God-like descendants of Earth or at least, Weyland-Yutani Galacticorp circa the year 10,000!!
This would be a 'get out of jail free' card for me because it then means that we, the viewer did not actually witness Earth's prehistory at all in this movie. Leaving the exact details of the creation of life intact.
Probably wont be the case tho