Hard to tell, technically Naruto should win... but because the story has to bee good he can't just go straight to SM or chakra mode and finish off Hidan in a split second this meaning that Hidan does have a chance to get Naruto's blood, at which point he could win... but again it has to be realistic, so Hidan wouldn't kill Naruto right away... this giving Naruto the chance to figure his powers out and do something.
In terms of power and abilities Naruto wins... if you want it to be a realistic (manga like) battle then it can go either way... it's Kishi's choice.