The cold truth is that it is thus inevitable that in the future humanity will need gene modification to avoid the spreading of harmful mutations. This is what they are doing here, especially since mitochondrial DNA is inherited directly from the mother means that any problems will be propagated to all future generation unlike normal genes.
There is still selection going on and it is difficult to argue that it is not natural. The pressures we are exposed to are just not consistent with some idealized natural state and thus seem "unnatural".
Be careful, "natural selection" is a specific descriptor that describes a selection process that is contrasted by "artificial selection". The second one comes up from time to time in human context; we call it "eugenics".
From this perspective, techniques that are technically eugenics, but can't feasibly be used in evil ways, are unambiguous progress. I'm wary of gene editing, but the technique described in the article doesn't seem like a slippery slope to me.
There are people who have a deep emotional need to control other people's lives and use all available tools to do that.
There are also people who don't have that need at all and would very much like to use the same tools to improve themselves or their children.
These are two separate groups but "we" are limiting the second group's access to tools in order to prevent the first group from misusing it.
In fact, some people tabooize the tools and intentionally attack even the second group for using them because they either afraid of the first group or, more often, because they are not even aware there are different types of people with different motivations and driving needs.