I’m wondering if someone is trying to make a play to get Fury removed as the leader of SHIELD. If they’re planning on doing it through political means, showing that one of his “favorites” is unreliable and prone to breaking secrecy and going rogue would put his judgement in question. If they’re planning on more direct action, weakening a team that is almost certain to be loyal to him would make him more vulnerable.
Plus, he pissed off some very powerful people by ignoring their “stupid ass decision”