Ummm
Reading through your sources, Cade, I think you've got this story a bit arse over tit.
Create a quick icon from Safari on your iPhone home screen and all that icon does is launch Safari at that URL. There's no difference in speed to opening Safari and typing in the URL, or using a bookmark.
However, Apple has provided custom bits of HTML which you can use to hide Safari's controls, if you want to use the full iOS screen (they've also added tags which let you do cool stuff like specify a startup image, which makes your web app even more "native-like").
For some reason, if you use the tag to make your app go full screen, Safari's new Javascript engine (Nitro) fails to work. This is pretty clearly a bug: If Apple wanted to kill off native web apps, it would be deprecating the HTML extensions and/or simply removing the ability to go full screen. Note that Android, for example, doesn't have equivalent extensions at all.
As for the whole UIWebView issue, again, this is a bug (or, more likely a security issue). As you note, some developers simply create native apps using HTML/Javascript and UIWebView, to sell through the app store. Why would Apple degrade that experience compared to online web apps deliberately, given that these apps deliver them revenue, when online ones don't?