In practice, this means you cannot actually put GPL applications on iOS unless you get a CLA from every developer on the project. This means a lot of perfectly good GPL-licensed applications will never actually get ported to iOS. You'll never see, say, Blender or Krita on iPad until and unless they CLA all their developers so that they can actually distribute the port legally.
If Blender Foundation or whoever runs Krita does have a CLA requirement for contributors, then consider that particular example corrected, but my point still stands: You should be able to distribute GPL software on the App Store and have the GPL terms supercede the App Store TOS.