What I got from it was that he's getting "we need to win with class" from pops and Harbaugh's saying "Let me do my thing". It's fun to bag on him but from reading the transcript it sounds like he was getting directives from ownership who are pretty disconnected to day to day operations of the team. They just want wins and no BS in the newspapers.
What I get from it is that York is implying that the 49ers would of been harsher with some of the idiots on the roster and Harbaugh over ruled them or objected. Now I have no clue if this is so, but if it is , shouldn't the guy that drafted these idiots be taking the fall? Harbaugh just wanted to put his best players that Baalke provided on the field.