I don't think the balls were altered, but I agree that the major problem with baseball is the owners. They have ignored every problem simply to generate higher profits -- don't get me wrong, I'm all for higher profits, but when the cheating becomes widespread enough, baseball will no longer be a sport, but simple entertainment like "professional" wrestling.
I've said for years that the only chance baseball has to restore its credibility is to get a legitimate commissioner. Bud Selig is a de facto owner who was appointed as "acting" commissioner and then after a few years baseball just dropped the acting portion since they never intended to even look for a truly impartial commissioner.
Then they can join the NBA, NFL & NASCAR.