Its true black swans are unpredictable but we can know to some degree which systems have risks that can eliminate the entire system. Biological systems are one of those because we've seen plagues and viruses come close. Financial systems as because of interdependence. What the article describes is an external modification to the gene line, which if you follow out a few generations, has permanent consequences on the entire gene pool.
This is overblown. Nearly all "the entire gene pool" lacks this particular mitochondrial defect. The population who have it, have a great deal of trouble reproducing. This procedure allows them to reproduce without passing on the defect. Unless some other trait has been previously limited to this population and will now be passed on to viable descendants at a higher rate, the effect is very small. Unless that particular trait is so advantageous that those descendants will outcompete all other humans, it certainly won't have "consequences on the entire gene pool."
