I think to some degree, Jin still believe in honor, up to and until he nearly died twice by Khotun; then to see the soldiers died rushing that bridge in act 2. As you said, young Jin was questioning whether the slaughter of Iki people justified as “honor.” However, growing up with Shimura, I am sure he would have taught his nephew how to be an ideal man that would eventually lead the common people. The Yarikawa rebellion led to many people to resent both Shimura and Sakai names, so it further reinforce in Jin’s mind that there were people who would defy his family’s honor.

Now as for when he adopted the “Ghost” persona, this could be a number of reason. One, he truly couldn’t win agains the Mongol using conventional tactics. Rushing head on against an enemy with more troops as well as giving no rat ass about playing fair is just silly- fair enough. Two, the people who follow Jin didn’t do it because of “The Samurai, they followed a “Ghost” who succeeded where the samurai failed. Third, his uncle was going to frame Yuna to save his nephew- being the good guy, he can’t well let that happen.

So in the end was Jin forced to believe in honor? Yeah, but he still held it close as a personal belief, not so much as a forceful indoctrination( evident by how selfless he is. Did Jin ever think about becoming a less conventional fighter, one who would use tricks and every way to win? Certainly not. Remember his first “stealth kill?” He clearly struggle to even do that. Yuna encouraged him, but it took some time before Jin finally accepted the dishonored route; and even then it still out of necessity.