Ben probably should have fought the suspension instead of accepting it (which was essentially an admission of guilt). Then again, the NFL's disciplinary procedures in regards to what he was suspended for are much more clearly defined in the collective bargaining agreement.
The thing with the Brady ruling is that it isn't about his guilt or innocence or the ethics of what he allegedly did; it's about Roger Goodell going beyond the disciplinary process that was collectively bargained with the union.
Edit: To complicate things further, Ben's suspension was given under the old contract wasn't it? TBH all I can remember about that situation is that he pretty clearly committed a crime and the responding officer decided to take selfies with Ben instead of taking the accuser's allegations seriously.