WHAT? The real security issue is that a website could own your device. Who cares that jailbreakers were using this to do something they wanted to do to their own devices, it could just as easily have been malicious.
You said: Once they do that, these vulnerabilities will no longer have a beneficial side to them.
I'm sorry, but what the heck are you talking about? I can think of a ton of vulnerabilities that would have a "beneficial" side to them. Say, for instance, a website were to install a key logger and capture all your passwords, or credit card numbers, or whatever... This vulnerability is far worse than simply allowing people to jailbreak their phones. It gives some other entity remote code execution to your device and that is pretty much the worst sort of vulnerability and Apple is right to patch it as quickly as possible. Period.