The fact that once one user reports the malware, apple can:

Revoke the developer's code signing keys Freeze the developer's payments Alert the authorities about the developer Revoke the app from the app store Push an "upgrade" notification to every registered user to remove the application Or even more drastic, engage the application kill switch

I'm really not sure how you think a fully managed software platform will have more malware problems than the run-arbitrary-code-off-the-internet system we have now. It seems like it's actually a killer solution to the problem.