That's exactly the point. His Grandmaster ordered it. Wanna remember another BS change on MK lore?
MKII: Kuai Liang is recognized as not being Scorpion's killer because the hellspawn spares the life of a fighter.
What do we see on MK9? "I would kill you. But that's not my purpose".
IMO, Scorpion & Sub-Zero (Bi-Han) story dealt with consequences. Hanzo is a legendary fighter, but as human he had lesser chances of beating Sub-Zero. So, Sub-Zero could have spared him (as Raiden would ask Scorpion on MK9) and by doing that he would save himself from having his killer. At the same time, he was saving himself from becoming Noob Saibot.
He could have easily picked the map, turned his back, and climbed up the rope. It would make no difference for him. But he has chosen to kill, and paid the price. That's exactly what the comics are dealign with: bloodshed and its consequences.
If now Bi-Han is not Hanzo's killer, that just breaks all the feedback process, and makes Sub-Zero a victim, Hanzo a victim/pawn and Quan Chi an a-hole. I prefer the original, where Bi-Han was an a-hole, but was innocent for one crime, and was unjustly murdered (because Scorpion wasn't caring for his death anymore, but for his family), Quan Chi made both toys, acquired The Amulet, used Scorpion, made him kill Bi-Han, created NS, turned Noob against Kuai Liang, fooled Shinnok and bested Shang Tsung as a-hole of the series.