"Lucy" was a famously well preserved member of the species Australopitcheus afarensis, not a memeber of genus Homo. The hominids seen in the series finale were definitely not A.afarensis. They were not H.neandertalis either. Too short hands for neanderthals, slim physique, walked in fully upright posture, and the geographic spread of neanderthal remains does not cover any parts of Africa. They were quite obviously (portrayed by) modern humans (H.sapiens sapiensis) and the most logical thing to assume would be that this is what they were - especially considering that the fleet humans were genetically compatible with them. Which is another can of worms and would suggest towards timetravel hypothesis... it's a better option than a divine hand as suggested by Baltar.
Mitochondrial eve is a term that is used to describe a common ancestory between all humanity due to a genetic bottleneck in human species in the distant past. It is estimated that at one point all of human species consisted of a few thousand people, who likely originated from one tribe that started to expand.
The assumption that Hera was the mitochondrial eve of humanity on this Earth doesn't work either, because there were a lot more females around in both ragtag fleet and the indigenous people. Moreover, Hera's mitochondrial DNA should - according to present day genetics - actually be cylon mitochondrial DNA from Athena/Number 8 line. And she could only be the true mitochondrial eve if all the other females' lineages simply ended at some point, which is... unlikely at best, and would seem to suggest to some problems that the colonial human females would have had with reproduction.
Even then it wouldn't explain why Hera's mitochondrial DNA would take over the mitochondrial DNA of the indigenous people already inhabiting the area.
Unless Cylon mitochondrial DNA comes originally from Earth that was found in the end...

It doesn't make sense. I think someone fails biology forever as well as astronomy, but it's no matter. It's also possible that the Smithsonian institute failed and just thought the remains to be of mitochondrial eve, but "Baltar" and "Caprica" knew better.
...however, if the remains were Hera's we now know that canonically Hera died young. Which is no surprise really, tribal community life expectancy is not really long.