Enterprise users can run their own "private app store" only if the apps will be used internally. The rationale is simple.
Apple develops and maintains the App Store infrastructure. Developers get to make money off of the public using apps hosted on the App Store. As far as Apple is concerned, developers are making money off of the public using a platform wholly owned by Apple. In my opinion, it is Apple's right to set limitations on how its App Store is used. Enterprise users, however, are not making any money off of the public. It is for their own internal use only. It's not a "legal jailbreak" at all.
Don't think of the App Store system in narrow terms as "I should be able to do whatever I want with my phone." Think of it from Apple's point of view. Apple is a business. With the App Store, developers are able to make money off of Apple's customers on Apple's turf. Under these circumstances, it is fair for Apple to regulate what takes place on its own turf.
Also, what exactly is a "legal jailbreak." In fact, who is stopping you from jailbreaking your phone? If you look at it properly, Apple isn't stopping you. All Apple is doing is telling you that there will be consequences if you jailbreak-the warranty is voided. How exactly does that translate to Apple "preventing" you from jailbreaking. The way I see it, every action has consequences. If you choose to take those actions, you have to face the consequences.