he doesn't become the leader of the clan, he's their pet and it's made clear that he did not sleep with the wife, and he gets shot up by the Gatling which only stopped firing because the imperial army stops firing.
Also, last samurai, like Gladiator and Dances with Wolves and a host of other historical fiction, never made any airs about being historically accurate.
It's still a crap movie but you don't need to make up sh1t to sell us on the movie's crappiness.