What's left for the people who aren't criminals but don't like being spied on? PGP and keys that are exchanged physically, by hand?
If somebody can physically spy on the infrastructure cables that your traffic goes through, will SSL protect you? As written in the article -- no it will not, because the certificate can be obtained, even if it takes some time and strong-arm effort to do so. But when a country can order you to give up private keys and keep quiet about it, really, what can you do?
At this point, full decentralization, mesh networking and something times better than Tor encoded in 100% of the network code seems to be the only way out. Maybe a combination of IPFS and FreeNet, full packet-level encryption and keys that expire in 1 minute and are auto-generated for every transaction?