Hannibal soon finds himself enrolled in medical school, where he uses sodium pentathol to help himself remember which Nazis killed his sister. Although this is a little more in keeping with his established character than the samurai stuff, it sets up the last half of the movie to be a smarmy, Inglorious Basterds-esque revenge fantasy.
"Please, no. I don't want to die in a movie this bad."
There was nothing particularly samurai-like about the portly European guy skulking around a jail cell in Silence Of The Lambs, so why include that? It all feels weird and unnecessary. Perhaps the explanation comes from the fact that Thomas Harris was bullied into writing the script by the movie's producer. So that's one way to never get asked to write a Hannibal story again. Heck, we're lucky his origin story wasn't something dumber. An alien, maybe. Or a Flintstone.