[teraflop]

As mentioned in the NYTimes article, a gene drive is more than simply introducing organisms with new traits into a population. It also codes for cellular machinery so that if the gene appears in one copy of a chromosome, it will splice itself into the other chromosome.

In other words, if an organism inherits one copy of the altered gene from either of its parents, nearly all of its descendants will also carry it. Which means that even a trait that is fairly detrimental to the organism's survival can spread through the population, in violation of what natural selection would predict. So, yes, we can "alter" a species.

[MiracleUser]

You are not emphasizing the descendants part enough. It still requires existing members of the species to propagate the gene with natural breeding, same as 'natural' genetic mutations. So if it is a gene detrimental to survival, it can still very easily die off. Which is not in violation of what natural selection would predict.