I don't see how providing the source to an open source app would kill the App Store. It would just add some cost that Apple doesn't want to pay.
As someone who has made public GPLv3 code, I am very happy about this. If my users can't send me patches that they've actually tested, they are useless.
"If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information"
The purpose of the anti-Tivoization provisions is to stop hardware vendors from including GPLv3 firmware in their device that they can update but you can't, and it is fairly narrowly tailored to try to accomplish that.
That's right, they could simply add a "unless the license specifically allows you to do so" line, wouldn't cost them much. I wonder how many gpl software there are on the app store.