As far sa the Qui-Gon reaction shot to Anakin meeting Obi-Wan, I'll take an unexplained grin over "YOU'RE a jedi TOO?? Pleased to meet you!" anyday. That line was unforgivably cringe-inducing.
Also, vis-a-vis Dooku leaving after taking out Obi-Wan and Anakin...I think the idea is that he's a Jedi, not a Sith in these fanedits. Thus, he has no reason to murder them; he only needs to neutralize them so he can make his escape. Their disagreement is primarily political, not religious.