It's not clear that Apple's particularly concerned with jailbreaking; instead, they want to ensure that:

1. They patch the bugs that, e.g., allow jailbreaking through a webpage or pdf (since those are genuine bugs could be used maliciously).

2. A device comes locked "out of the box", and can only run signed code (so that the vast majority of people need to use the App store).

3. They don't have to support jailbroken devices (so if you install an app on your jailbroken phone that doesn't play nice, it's not their problem).