On the one hand, the author is absolutely right that a good professional designer can bring things to the process that enthusiastic amateurs cannot. A really good logo doesn't just look cool, it communicates something about the nature and spirit of the company visually. It lays down a marker: "this is who we are." A designer who knows the grammar of visual communication will have a better chance of delivering that than will someone who doesn't.
On the other hand, the author sadly doesn't do a great job of arguing the above point. Rather than, say, taking some great logos and pulling them apart for us to show how they do what they do, we just hear a lot of complaints about how the way Yahoo did theirs was "unprofessional." It makes it sound like the main complaint is that Yahoo had the gall to cut designers out of the process rather than that they chose a path that was more likely to result in a crappy logo, which strikes me as a more powerful (and accurate) complaint.
In other words, outside the community of professional designers, nobody cares if Marissa Mayer hurt some designers' feelings. What they care about is how Marissa Mayer is stewarding the Yahoo brand. If you want to convince them that your way is right and her way is wrong, don't show them how her way threatens your business; show them how her way threatens her business.