How about this, it doesn't matter how they died. You do see Anakin's spirit at the end of Jedi. The only conclusion one could draw from this is that only those that have good in them, remain. Vader still had some good in him, and thus his spirit remained behind. So now you say, well Qui-Gon was good and I didn't see his spirit. Well the only thing I can think of is when Obi-Wan is asking him not to go against the council again. One might could conclude that Qui-Gon isn't such a great guy, and maybe even a troublemaker. Maybe the virgence in the force wasn't anakin but rather Qui-Gon, and maybe he's the reason Anakin turned into Darth. But now it's just all supposition.