There's no question that understanding the mechanics behind these frameworks will yield much better apps, even if you skip out and go barebones jQuery. But there's always going to be a tradeoff between writing all the boilerplate and structure yourself, rather than relying on a framework to lessen the burden. With emberjs, you get immensely reduced boilerplate and some pretty sound opinions on structure. If you want to exchange writing more code for less of an opinion and more flexibility, then go with backbonejs.
Each of these frameworks bring key strengths to the table, having been written by amazing devs (like Yehuda Katz) with the additional benefit of "community consensus" to boost their usefulness. The article makes valid points, but keep in mind there's definitely more to this story.