I severely doubt that big corps will force side loading their app in iPhone when the easier experience is the iOS AppStore. Same reason why all those apps you mentioned are in the android store and not just apk downloads from their site.
So say you want WhatsApp on your phone.
Today: AppStore - get WhatsApp.
Tomorrow: AppStore - get Facebook store - start Facebook store - get WhatsApp.
The power Facebook (also, Microsoft and Google) have over the users of their apps may be so great that they could pull it.
Small companies? No chance in hell.
So actually, this move might put Apple (and Apple users) into a weaker situation while empowering FB/MS/GOOG and having no effect whatsoever on small app developers.