There's absolutely no reason that Apple wouldn't be able to allow GPL apps legally on their app store. It's just a matter of Apple changing their own terms.
> The GPL could make an exception for app stores
No, it couldn't unless you have a time machine or the ability to get consent from the author every line of GPL code ever written to agree to relicense their code under these new terms.
Apple doesn't even need to make exceptions for the GPL, it could just relax its policy or allow users to install whatever software they want.
You can read more about those terms here[2], but they have nothing to do with the iOS security model.
[1] http://adium.im/pipermail/devel_adium.im/2011-January/007973...
[2] https://www.engadget.com/2011-01-09-the-gpl-the-app-store-an...
The GPL is fundamentally at odds with a lot of things, for $reasons. For example, ruby could not be distributed with compiled-in OpenSSL support, until the developers adopted an OpenSSL linking exception.
The GPL or the developers of the GPL’ed software could make an exception for app stores. But the developers have deliberately chosen a license that is incompatible with certain uses, including all app stores - it’s not only the apple App Store that is affected, all consoles for example are affected, too.