Except this particular vulnerability has precisely nothing to do with jailbreaking. To the contrary, it's a flaw with Apple's own way for enterprise customers to install unapproved apps.
While your first sentence is reasonable, (but strictly speaking, does not actually negate anything I said, aside from implying a minimization of the relevancy of my comment) your second sentence is technically incorrect: The enterprise certs are working exactly as they were intended. The real issue is that a malicious entity happened to obtain access to such certs. So the questions are: How did they obtain the certs? And how can Apple prevent future compromises of this nature?
If we apply Hanlon's Razor, I'd think it's a pretty good bet that the malicious entity simply signed up for the developer program, themselves. Thus, the easiest way that Apple could stop that from happening in the future is to increase developer fees, which would unfortunately also have the negative side effect of locking out smaller iOS developers entirely. Finding the threshold at which malicious entity interest is minimized, while also minimizing the discouragement of legitimate small developers, is obviously a calculated balancing act... but will never be entirely foolproof. The fact that this kind of malicious act has only been reported this once suggests that Apple has a pretty clear idea of what they're doing.
In any case, it seems pretty clear that Apple has already revoked the certs and suspended the developer account in question, so this particular hack is effectively in the clean-up phase now.
(The rest of your response just sounds to me like the usual soapbox "Apple bad! Big business bad! They're all out to get the little guy!" commentary, so I seriously doubt that anything I could say is going to dissuade you from your point of view. Suffice to say, we'll just have to agree to disagree.)