This totally misses the main point: Apple could absolutely have brought this up within a reasonable amount of time. The issue here is reliance.

Granting app store approval to an app encourages the company to build around the app and around the brand. And Apple gave that approval for many years. And then, after all that time, decided that the brand is projecting an ethos that they don't approve of?

Apple's process doesn't just involve tacit approval. It's very active. They had so many opportunities to not give approval, to not hit the button, but they did and for quite a long time.