I've been following this since I heard of it happening- definitely interesting. I like the idea of a custom CMS to avoid an open one (more security).
Sadly the moral of the story is the exact opposite - the custom CMS HBGary commissioned was actually less secure, as it appears not to have been subjected to proper security audits, nor was it being updated to patch discovered bugs. Direct from TFA:
Rather than using an off-the-shelf CMS (of which there are many, used in the many blogs and news sites that exist on the Web), HBGary—for reasons best known to its staff—decided to commission a custom CMS system from a third-party developer. Unfortunately for HBGary, this third-party CMS was poorly written. In fact, it had what can only be described as a pretty gaping bug in it. A standard, off-the-shelf CMS would be no panacea in this regard—security flaws crop up in all of them from time to time—but it would have the advantage of many thousands of users and regular bugfixes, resulting in a much lesser chance of extant security flaws.
The very thing you consider a disadvantage in an open software system - the fact that anyone can discover bugs in it - also helps ensure that such bugs are publicized and fixed. With HBGary's custom CMS, the bugs were still there, but the only people looking were the ones specifically trying to break into their system. There can be a case for code obscurity, but if that's all you're relying on to protect yourself, I'd say you're really just burying your head in the sand.