I find the article a little overzealous; while I'm no staunch capitalist, including sentences like "The web in its current, open state is a threat to capitalist ideals" doesn't help convince me about your goals.
And yes, while this is partially true, a lot of legitimate businesses and people who aren't motivated enough to "go dark" also drive the internet, and they're not going to be so easily forced underground - any such internet would be a shadow of its former self, and an easy thing for governments to demonise with the usual examples (drug trafficking, child pornography, etc.)