First lets not generalize, as not everyone that jailbreaks a phone does that to install pirated apps. There is a legitimate reason to do it, that is to gain finer a better control of *your* device. So the "dark" side is not related to jailbreaking, but rather to one's own tendency to perform illicit acts.
Jailbreaking is just one of the many steps that are used to allow app piracy.
As for the article, although the overall concepts are correct, there is one tecnical mistake and a few misconceptions.
First, it's not a kernel patch that enables running and installing pirated Apps, but rather a patch to Apple's App installer. The kernel is patched during jailbreak to allow software signed by other to run, and yes, the pirated Apps take adavantage of this legitimate feature too.
One issue is that some members of the community expect Apple to handle the issue and create a system that is piracy free. Well, let me ask: do you know any platform that is like that? For example, Microsoft redesigned Windows 7 activation and months before it was released to the shelves, there were a few programs floating around to circumvent their activation.
In fact, Apple futile attempts to make it as tight as possible is what is hurting them: the code is so complex that it leaves many vulnerabilities to be exploited.
Like with other OSes, the software designer can take some "clever" steps to minimize piracy chances. Even on iPhoneOS there are several ways to do it, some simpler to spot, some not so easy. I know of a few popular apps that never showed on .... well, you know where
So, instead of complaining, software designers can take action. Can Apple help? Yes, they could change some details on their approach that would make it simpler for programmers to check for pirated code.
But, software piracy will always exist. There is always someone willing to spend some time doing reverse engineering to figure it out.
For those that seek absolute protection against code piracy, there is one simple and effective approach: do not write code.