This is a judgement of the motives of Apple that I do not believe is correct by Stallman and he making a straw man case for it. I don't think that Apple "hates" their freedom.
I do believe Apple added the restrictions on having only non-GPL code because they understand the problems that it presents legally in the App Store as a distributor and their bourdon under the GPL by being the middle man and redistributing the software in question. Apple would be required to field GPL requests for software in the App Store as the main distributor. This is risk and overhead Apple doesn't want to deal with.
They could just as easily make the language not specifically mention GPL at all but instead say that you releasing software on the App Store can't add restrictions, constraints, or additional requirements on how Apple distributes your apps in the App Store not expressly contained the agreement already. This would be the same and would be just as GPL incompatible as it is today.