This is my problem with the article. It feels like it suffers from a bit of zero-sum fallacy. The statement here is, "it can be broken therefore it's fundamentally broken." I think it's more useful to think in terms of probabilities. If I disable password authentication for SSH and require public key authentication on my web server, an attacker can still get in by stealing my private key. That isn't a reason to take the opposite approach however - botnets commonly employ password-guessing attacks against entire IP ranges so you're not actually safer by avoiding this practice just because it isn't a perfect solution. There is no silver bullet for security, only endless layers of strategies and adaptations to edge cases.
I did enjoy some of the points about the limitations of email encryption (the email chain example is a great reminder of how security is often more about human behavior than software). But I think the article could have been more compelling had it presented a less dogmatic thesis - perhaps "Email Encryption Won't Save You" or something like that.