Like the article says, Instagram is absolutely an escape from the hostile interfaces and hostile posts that abound on core Facebook. It's still cool and it's still fun. Whatever the internal power dynamics, it seems unlikely that Facebook would be stupid enough to throw this away. What do they care if their bread gets buttered through the Instagram app?
Another interesting thing to note about Instagram is that a high follower count has become a status symbol. As people invest time and effort in building a large following, their commitment to the platform increases. It wouldn't surprise me if Instagram accounts for more than half of Facebook's value in the near future.