Consider the two-dimensional graph of difficulty of hostile interception of traffic vs. the value of hostile interception of traffic to the intercepting entity. ("Interception" including both attacking authenticity and privacy of the connection.) In the low/low side, you have, say, my blog posts. Deliberately public, of interest to pretty much nobody "official", unencrypted, unauthenticated HTTP. On the high/high side, well-encrypted inter-colo traffic between two computers owned by a bank, or perhaps an arms manufacturer.
10 years ago, this was a rich graph with lots of interesting nuances. Who even cares about the easy/easy cases? Of course the hard/hard cases justify encryption. And there's a lot of in between and useful cost/benefit analysis that could be done. I think the original article is written based on this mental conception of the landscape.
However, recently between technological advances and increased discovery about what is being done by governments (and remember, not just the US government, many have been caught doing things and many more are presumably getting away with things we still have not heard about) and a variety of corporations (and remember all this Superfish stuff and such predates the mandatory encryption!) has revealed that the previously-rich 2D landscape really isn't 2D after. It turns out that there is no "difficulty" dimension. It's all very easy to intercept, at scale, if not downright trivial. Governments hoover (both the vacuum and as in J. Edgar) up entire fiber optic trunks. Companies and spyware get a footprint on a machine and basically nuke all SSL flat for thousands of machines or entire major corporations at a time.
In the other dimension, it has become pretty clear that even "trivial metadata" allows far more information to be exposed about someone than any but a handful of computer scientists would have believed 10 years ago [1]. Everything has a great deal more value than we thought.
The net effect of all of this is that it collapses the entire previously-two-dimensional landscape to a nearly a single point. Everything is trivial to collect, and everything leaks a shocking amount of information, and information is power.
Consequently, regardless of the fact that both answers suck in their own way, we really only have one choice: Require encryption, or not. There's no middle ground anymore. We used to have one, but it's collapsed away.
And, frankly, acknowledging everything in the original article and with the amplification that there's probably even some stuff missing that could be added, I'm pretty sure that in the end, there's still only one reasonable choice, which is the direction we're currently headed in. Yeah, it sucks. But a root cause analysis of the problem isn't that it's the encryption's fault... it's the companies, spyware, and government that have put in so very, very much effort into collapsing this landscape. Blame them for the measures we have to take to protect everybody.
Though, even as you do so, bear in mind that in the rich, complex ecosystem of the Internet, parasites are ultimately inevitable, so it's also no use pretending that if we just fix the current companies and governments we could somehow change the problems. The only answer is that, yeah, we have to rewrite how the "laws of physics" of this ecosystem work. The only other alternative is the overproliferation of parasites and a resulting value collapse of the ecosystem to humanity as it becomes too untrustworthy to use for a variety of things we'd really like to use it for. (That is, I'm not claiming that the Internet would become entirely useless, but we'd really like to be able to use it for important things, not just Buzzfeed and cat videos.)