Going his own route doesn't mean he wasn't one of these goody-goodies the prequel era was full of. You could see him trying so hard at being this moral wisey wisey nicey nicey Jedi. Alec Guinness's Kenobi never made that sort of effort.
notice he tried to free Anakin's mother, (and logically, bring her with them) which totally went against the Jedi's rules of attatchment. I think Qui-gon knew what would happen to the Jedi if they didn't change, and his death prevented him from introducing that renassiance (the role which eventually fell to Luke.)