One of Pope Francis's methods seems to be to marginalise the awkward squad. 
Is Muller a 'senior cabinet official'? As Pope, Francis has always down-played the CDF. Muller has been made far less important than his predecessors ever were. For example, Muller was not appointed to the C9 group of cardinals. What an omission for a Congregation which likes to think it is the very centre of power.
You are right on the 'censorship' front.
So far as Muller keeping his job:- His imminent departure from it has been touted for what seems like very many months. But here Muller still is. So perhaps Francis is happy to keep Muller in place at the CDF, confident that Muller can't (or won't) do or say anything very much? Perhaps it is Muller who has been censored?