A holy shitstorm? But it won't happen. The same logic would apply to apps from other fierce competition, e.g. Google Maps and Skype. While there have been some occasional issues with upgrades being rejected, the apps have been allowed to remain on the store.
The more contentious issue is with builtin apps and platform capabilities, e.g. it's possible Apple's map could show directions and prompt a one-click Didi ride. Google already does something like that with Uber, but it could be even more tightly integrated with payments, and in a way that the platform could favour certain providers.