They own Lucasfilm now yes. But they leave their various companies to mange themselves. It basically comes down to Disney ordering a bunch of movies and then leaving Lucasfilm alone to their own devices as to how to go about it.
Same as how Kevin Feige runs Marvel Studios. He's the one calling all the shots and Disney is basically just the distributor.
Bob Iger made it clear that when he buys a company, he's also buying the management because he knows they're essential to the continued success of that company.
The decision in regards to the EU was purely an internal one and Disney had no part in it.