It's a difficult one as it seems almost certain that none of the players or managers were aware, and any punishment will affect them and the fans the most. It's all been led by the owners, and they're the ones that need punishing.
Ideally, FIFA/UEFA/whoever would have some sort of jurisdiction to kick them all out with pretty much immediate effect and ban them from ever being involved in the running of a footballing entity ever again. Then, right from the top we can start looking at proper regulations regarding the ownership of clubs.
In reality, the clubs are likely too valuable to their leagues and UEFA to do anything drastic, but I also feel like you couldn't have too many complaints if all of the clubs involved were banned from European competition for a number of years, and potentially even expelled from their respective leagues. I don't know how it works in Spain and Italy, but here it would mean expulsion from the PL, at which point I guess they'd be free to apply for entry into the Football League, failing that the National League, and failing that, whatever body is in charge of levels 7 down.