The inability of binaries to do malicious things on iOS is the result of the sandboxing and entitlement mechanisms of the platform. The store review and approval process is what stops applications from including entitlements that undermine the platform security. If you remove that step from the process there is nothing stopping an application shipping with the system entitlements that allow the application to read or write to other app data, or the entitlements to talk to system services without prompting permission dialogs, etc.
If you want to remove the review and approval systems that the App Store has (and it sounds like are going to be required for 3rd party stores?) you have to have an answer for that. Otherwise you just end up with the android malware problem.