No, it's not a wild conspiracy theory and there was never any official news. There was a Facebook engineer giving a PR approved version that is designed to minimize the issue.
The entire timeline is exactly what would be expected if Apple told them to change the app or get removed. Apple does not pull apps immediately for situations like this, nor do they comment. The times we hear about Apple threatening app removal in the news, is when the developer goes public because they disagree with the decision and think they can score PR points. Apple has never joined that fray, even when they look bad and have to reverse decisions like they did with a few apps after iOS 8 was released.
As to how long it has been there, every indication is that it has been present for months if not years. This is not new to iOS 9, the ability for the user to look in the battery menu to see what is happening is new to iOS 9.
That's a lot of assumptions on how apple deals with 3rd parties . You maybe correct, I have doubts though.
iOS 8 showed battery usage by app, so it was not introduced before iOS 9, as users would have complained, as hey did when it was discovered, it was obvious Facebook was causing a batter drain.
I've seen apple longer to fix bugs to be honest, so still not sold on the theory that Facebook got caught.