Gentle fist can disable Narutos arms, but a single hit from Naruto is deadly as well and could kill or knock Neji out. So depends on who hits first? no, if Neji hits first Naruto can still fight with his other arm or legs, if Naruto hits first thats it for Neji.
SM Naruto will win. Also frog kata can use the Natural energy around them, so the range and force of Naruto's attacks are extended, Neji can't dodge this, while Naruto's sensing abilities help him to dodge Neji's attacks.