I seriously doubt Apple ever intended to let web apps as the only means for open iphone app development. They probably planned the SDK before iphone's even released. The "web" as app is probably just an excuse to buy time.
The whole matter seems pretty straight forward to me - Apple don't want to have 'just another phone' that can run the same Java and Flash and cross-compiled apps as every other phone, they want to leverage their market lead to pressure developers into focusing on iPhone development at the expense of other platforms. It's a pretty logical, inevitable outcome of the business situation.
Maybe Android is the real target:
"Minority platforms are always going to be the biggest beneficiaries of cross-platform development."