End to end encryption is the only answer here. Maybe instead of relying on server certificates, which could be compromised, do the reverse -- the client certificate is used to secure the connection. That way everyone can use a CA (or even issue their own) that they trust.
Have you looked at the work going on in the IETF and other places to deploy "perfect forward secrecy?" The idea is to use a Diffie-Hellman exchange to negotiate a random key, and then only use the server certificate to prove the server's identity and knowledge of the key. Pretty much the same result as client certificates, easier to deploy, and with the added advantage that even if the server's key is compromised, the sessions' keys remain secret.
Link to Original Source
What this story really exposes is the hubris of the inventor. Say you work a couple of months on an invention, and file a patent. Do you really expect years and years of revenue? Really?
We have seen attacks like that before, e.g. the "Comodo" hacker (http://arstechnica.com/security/2011/09/comodo-hacker-i-hacked-diginotar-too-other-cas-breached/). My bet is that we will continue to see more of these, because the attack surface is just too large.
On the other hand, if you are accepted in the Legion, you will have a fun time in places like Afghanistan, Djibouti or the Ivory Coast, to name a few. If you goal was to escape being shot at, you may want to reconsider.
Consider for example what happen to Wi-Fi. The IEEE has a fairly detailed patent policy, and the Wi-Fi standards have been very successful. But after millions of cards were sold, CSIRO came out of the blue and asserted a patent on indoor OFDM that they said covered Wi-Fi. The resulting lawsuits have costed millions.
The list of password that the worm tries is interesting. Apart from the obvious abc123 and the like, the worm tries "RavMonD" and "zhudongfangyu". Is that a clue? Some Chinese hommage to the bazar?