Wired has an interview with the authors of a book titled, The Science of Battlestar Galactica. I wasn't a viewer of the show, so I wasn't aware that the mitochondrial Eve scenario turned out to be a major plot point in the series' finale. Wired chose to excerpt that part of the book.
The excerpt does a good job differentiating the most recent ancestor of humans from the most recent ancestor in the exclusively maternal line -- the mitochondrial Eve:
It’s important to emphasize that Mitochondrial Eve and her contemporaries had offspring, and those offspring had other offspring. But throughout the subsequent generations, for one reason or another, the lineages of Eve’s contemporaries all died out. Of all the women alive then (and in our case, that means the entire female population of Galactica and the fleet), only one has offspring alive today. We know her as Hera Agathonv.
This does not necessarily mean that Hera is our Most Recent Common Ancestor (MRCA). Hera populated today’s Earth solely through her daughters and daughters’ daughters. The MRCA is the person who, while no doubt descended from Hera, populated today’s Earth via their daughters and/or sons. By adding males to the mix, the MRCA almost certainly cannot be the same as Mitochondrial Eve. In fact, most researchers today feel that the MRCA lived only about five thousand years ago, 145,000 years after Hera.
That's a good two-paragraph summary of the issue, though it could use more fleshing out. Unfortunately, the book excerpt goes off on a Toba tangent, discussing the near-extinction of our species as a "real population bottleneck."
This is a hard part of population genetics to get right, the distinction between effective and census population size, and the relationship between demographic events (like bottlenecks) and heterozygosity. A good description of the science should be appropriately skeptical -- I would expect no less for various "faster than light" drive technologies, which surely are harder to explain than population models. In this case, the reconstruction of population bottlenecks is highly speculative, and there is positive evidence against the Toba scenario having been a catastrophic event on the scale described here.
Still, I don't have any problem with a science fiction series making use of such a scenario as a plot element. It's the perfect kind of thing for fiction. Beats the heck out of "midichlorians"!