I am an Android fanboy. There is no such thing as a secure app store. When you use a PC, you are already exposed to the wild west and the best anti virus in the world is actually you the user and this incident with Apple proves just that.
I don't believe the Apple app store is 100% secure because it just isn't possible to vet every single app in the review process in detail. I treat it to he just as secure as the Play Store. Beeper was able to exploit iMessage on Android suggesting that was having vulnerabilities as well.
You could argue we are seeing only 1-2 shady apps and Apple is stopping 1,000 of them while third party stores probably wouldn't do anything.
But here is the thing. People trust the App Store. People would not trust third party stores. Android specifically warns you when sideloading any app and the user is well aware of the risks. Apple is providing a false sense of security on their App Store so a user may not even use basic common sense when downloading any app from it.
It's like this. If I know an alley is dangerous and I am at risk of getting mugged, I would avoid it or at the very least ensure I have some protection when going through it. If someone assures me that an alley is safe, I wouldn't think twice walking through.
This incident neither supports nor weakens Apple position. Nothing is safe. It's upto the user to use basic common sense.