I see no reason to blame the educational system for the death of free thinking. I think parents and schools work in concert to over protect children from the realities of the world. A few years of college is usually enough to shake it off however. Rather, I would have to say the death of free thinking is societies fault because that is where the real damage is done. In society you constantly see people shriek away from things that are different or they're quick to judge a person or brow beat them. This is what kills free thinking, not education systems.
This is a question that both answers have some validity to. While free thinking isn't completely dead, the "you do X because X is what you do" of education plus the "everybody has to be a winner" of society have combined for a world that nobody has to blaze their own trail anymore. We're so afraid to tell anybody that they failed that it has resulted in a world that largely discourages unconventional thought because it's easier to just say what's agreeable.
Unfortunately, society as a whole can be blamed for the death of free thinking. Companies and corporations constantly tell Americans what to think and believe. The same applies to politicians and other organizations. Free thinking is far less potent than it used to be because so many people can't think freely.
Education is not really to blame for the death of free thinking. I've been an educator for a long time and we teach our kids to think for themselves and to come up with their own conclusions. However, in society it is cooler to focus more on the next reality show or talent show or music artists than it is to create anything new or think freely. Society is to blame.
We should blame the educational system for the death of free thought in society, because the education system is designed for and encourages every one to be the same. The person who does best in the education system is slightly better than average. Society encourages free thinking, because society is a free market system in which the most innovative people still thrive.