At the end of The Big Bang, the Doctor asks River Song who she is and she says, "You're going to find out very soon now, and I'm sorry but that's when everything changes."
We've seen him find out who River Song is. While he went through a really rough time, and some conditions were different, not everything changed. It's true that he realized he had become a legend, and was known for violence (which is ironic, since he usually avoids violence). He also faked his death, so people would think he was dead.
This may lead to him either having to keep a low profile from then on, or to him working to come off in a more positive light, but it doesn't seem as earth-shattering (or Galifrey-shattering) as River makes it out to be when she ominously says, "That's when everything changes."
He still has his tardis and can still do pretty much whatever he wants. So what did change when "everything" changed?