Obi Wan made up the “cover story” of Vader killing Anakin to save Luke from the truth until he was ready. All of the Jedi knew that Anakin=Vader; however, Vader killed all of the Jedi except Obi Wan and Yoda, who managed to hide. I assume that that little tidbit of trivia died with them - or no one else really cared. In fact, it looks like Yoda knew in TPM, well, maybe not “knew”, but he had a good idea of what is going to happen.
As far as Qui-Gon, he may have been prepared to become ‘one with the force’. He was meditating while Darth Maul and Obi Wan were stalking around getting ready to fight. He didn’t disappear like Obi Wan or Yoda, but I still think that it leaves enough leeway for George to do what he wants with Qui-Gon in the future.