The "section 3.3.1" issue is just another in a long line of events that have the same basic shape: actions taken by Apple in what it believes to be the best interest of its platform (and, by extension, itself) that run afoul of the interests and opinions of developers. Any Apple follower can surely list others: the lack of Flash on the iPhone, the App Store as the sole gateway for iPhone applications, deprecating Carbon, and on and on.
Apple's decisions regarding its mobile platform in particular have been extremely protective from the very start. Cumulatively, these actions represent a huge bet placed by Apple. The proposition is this: Apple is betting it can grow its platform fast enough, using any means necessary, that developers will stick around despite all the hardships and shoddy treatment. Each time it chooses to do what it thinks is best for the future of the iPhone OS platform instead of what will please developers, Apple is pushing more chips into the pot.