But in the end he is still going to lose.
Concern over criminal behavior--i.e. Aaron Hernandez-- in the NFL has forced teams to take notice and act. Desean Jackson was cut for being hard to work with and due to concern the company he kept was going to get him in trouble. In the end the perception was that his me-first attitude was the real issue, but teams work with prima donnas all the time.
Why should he be any different as long as he produces (and he was)?
As exciting a player as he is the 49ers now have reason to be concerned about Kaepernick. The drug connection is being overlooked in the media, but the organization probably hasn't done so. Assuming that he is not charged with anything he is still going to look like a guy that was in a questionable moral position.
At least that is what the team is going to tell him when they say they want to wait till next off-season to negotiate his contract extension.