You say he is clearly injured, has a doctor ruled him out. Yes he is less than 100%, who knows what percentage he is. In this case as it has been pointed out, they are acting no differently than they have in the past with Buxton or any other player in this situation. You can't just put a player on the IL if the doctors are clearing him to play, you have to work with him if he thinks he can play, especially when it is your franchise player. He has shown in the last few days that he can play, Monday night was the most recent example.
Now I would have the conversation with him and convince him he is not helping the team. Last night was the final straw for me, if he can't run a ball down in the gap and is going to be out x number of days even if it is less than the length of an IL stint, he needs to go on the IL. Because he is not helping the team. But you are going to need his buy in.