Not doing anything might be worse. Within a month, all major money-making apps would make a similar move, hiding the functionality from Apple’s review process and then activating it once most of their users have upgraded.
Apple could spend time and money trying to find such hidden features, but that would mean many major apps would see no updates. That’s a losing game, too, even if they are successful at detecting such hidden functionality.
They must have thought about this and decided this is their optimal initial response (it need not be the final one. They can put the app back in their store in seconds)
I can understand that. Allowing this is guaranteeing the end of the App Store. Fighting gives them a chance salvaging it, parts of it, or at least, delay the inevitable.