Full disclosure: I work for Google. However, this blog reflects my personal opinions only.
Programming and computer science are not synonymous, but obviously the two are deeply intertwined. The fundamental activity of programming is the construction of abstractions. Programming language design and implementation is one of the fundamental forms of abstraction building. It is central to the field, and has been so nearly since its inception. One of the oldest and most important research conferences in computer science is named Programming Language Design and Implementation.
This suggests a particular understanding of what Section 3.3.1 means. Section 3.3.1 says: "Thou shalt not build abstractions other than those we prescribe." It bans one of the fundamental activities of programming.
This would be a mere curiosity, except for Apple's unusually influential position in the computing industry. All trends point towards mobile devices* becoming much more pervasive than all other general-purpose computing devices. Indeed, the combination of mobile and cloud computing may someday replace all other user-visible hardware except what's needed to support input and output (screens, cameras, etc.). And Apple has the credible goal of becoming the preeminent mobile device provider, setting standards for the industry and defining the entire computing experience for a huge swath of future computer users.
Section 3.3.1 therefore constitutes a direct attack on computer science, delivered by a powerful and well-funded organization that aims to transform laypeople's interface to the field. As long as 3.3.1 stands, for a computer scientist to purchase an iPhone or iPad is akin to a biologist purchasing a textbook that advocates against teaching evolution. Full stop. Go ahead and do it if you can't resist the shiny, but understand the moral weight of the decision you're making.
I can already hear people ready to trot out the standard roster of excuses. Hit the comment box if you want, but realize that I've anticipated the common objections and the only thing stopping me from preemptively rebutting them all is the fact that I'm moving soon and I have a huge number of boxes to pack. To pick just three examples:
Q: "The iPad isn't for people like you. Why do you care?"
A: "This post isn't for people who don't care. Why are you reading it?"
Q: "Apple has a right to do whatever it wants with its platform. If you don't like it, you shouldn't use it."
A: "Thank you for agreeing with me."
Q: "You can program whatever you want in HTML5 and access it through Safari."
A: "Yes, the web is an open platform, which Apple fortunately does not control.** I'm talking about Apple's rules for programming on the platform that it does control."