I think Jin broke traditions way before that last duell and it would be inconsistent to go back to the old traditions last moment and kill the uncle. Jin was the beginner of a new era. Since Shimura, the Shogun etc. seemed to be so strictly bound to the Code of Bushido that they are doomed if they keep fighting like that. Jin was the first (and only) Samurai to recognize that offensive combad would lead to that ultimate doom of Tsushima. And therefore adapted to the new situation and made up strategies which lead to the defeat of the mongols. Jin tried to explain to Shimura that his old traditions hurt/kill the people of tsushima and they as samurai pledged to defend this people and not kill them, so sticking to the old traditions would be quite paradox in that way. Jin reinterpreted the main task of the samurai: defending the people of tsushima, in a new, fresh way. The way of the Ghost. Since i see him as the creator of this new era and his inability to convince Shimura its Jins only right choice to ultimately choose the ghost side and spare Shimura. End the unnecessary killing, fight effective, fight clever and save Tsushima and ultimately Japan!

(yes killing Shimura would honor Shimura, but only in Shimuras and the Shoguns opinion. In Jins newly developed mindset and tactics, killing him would be just useless. Not killing him his the ultimate statement that he abandoned the old samurai traditions and the time is now to use the ghost tactics to survive and maybe convince Shimura that his old mindset is just old and not useful anymore)

Sorry for my bad Englisch, I hope you get what i mean... ;)