Flick is somewhat non confrontational when it comes to player sales. It seems to me he doesn't like to get involved in it and probably other than giving the club his recommendations, he keeps out of transfer business.
He is nice to the squad, as players have said, he is considerate of all including the ones who don't play and is usually positive when asked about any player.
That is a great thing about him and its why the players love playing for him, but it might also be why its harder for certain players to leave as Flick wouldn't freeze them out even if they aren't needed (eg Casado).
Araujo needs to be told that he won't play and to find a new club, if there are good offers then he needs to be removed without question but I don't think this is how Flick likes to run the locker room. So it would have to be the club doing it.