I'd argue that perpetuating the problem of people being treated different in society is even worse.

But middle-class white men are disproportionately encouraged to be programmers. As the article points out: "There were very few women and nobody of color. I found that puzzling since the startup industry was obviously booming." So to be fair, we should either stop encouraging them, or start encouraging people who are outside that group.

Seems to be it would be more productive to try to encourage more than a minority of a minority, as it were. Female programmers are already rare, blacks more so just by statistics. What about other races? Hispanic women are out of luck? Asian? Native?

That isn't a singular problem. Helping a group is not just another way of discriminating against them. Just as slapping someone's face is not just another way of kissing them.