The way I see it, Apple wants these WebApps to eventually be
Widgets for the iPhone.
Dashboard Widgets are created using a mix of HTML, JavaScript, and CSS.
Most apps on the phone seem like Widgets to me, especially Weather, Stocks, and Calculator. That makes me think that the iPhone has something similar to the Dashboard server. It probably does, with the claims of it running a true version of OS X. If these WebApps could be developed according to Widget instance standards, I think we'd have the right kind of secure apps that Apple is hoping for. It would be nice to hear this conformation from Apple, though.
I find it funny that people are already dismissing the possibilities of this less-than-four-month-old phone, based on them not completely opening it up. Hopefully apps will make their way to the phone in the form of Widgets, and hopefully we'll see some kind of a home button in a future iPhone update, maybe even a browser/installer to access these.