The problem is that Goodell then responded by doling out punishment (4-game suspension) that wasn't legally defensible, in spite of his broad powers granted by the CBA.

Even with yesterday's victory in court, Brady probably would still be better off if he had immediately said (right after the AFC title game) that there may have been some ball boys who went too far in deflating footballs without his knowledge. End of story. Maybe pay a fine. Move on with legacy fully in tact. The problem is that may have seemed risky at the time, given that the Super Bowl was approaching.