I think Apple's reasoning behind this policy is pretty simple: If you want to develop cross-platform applications then build web apps.
Section 3.3.1 is the middle ground between Apple's policy when the iPhone was first released in 2007 and the policy that existed prior to 3.3.1. Remember that entire year that we begged for the ability to write native apps?
Now Apple is partially rolling back their policy and cutting out 3rd party development tools for native apps, but at the same time (whether they realize it or not) they are pushing the web as their preferred platform for cross-platform application development.
There are legitimate negative consequences associated with the 3.3.1 policy, but I think it's hard to argue with the fact that a policy like this is good for the future of web applications and improving the web as a development platform.