Upon rewatching this episode, I still like it. The only flaw I see it is that in trying to homage UXM #172-173 (where Silver Samurai and Viper poison the X-Men aside for Logan, Rogue, and I believe Storm), they intentionally or unintentionally made the X-Men into jobbers, losing to ninja that Wolverine can pummel five at a time (Rogue does as well, for a while). In some ways it clashes about as often as when the show makes those obvious, and usually awkward, moments, lines, or scenes where they want to basically say, "Logan superior, Cyclops inferior" that seem tacked on and choppy.
Arsenal from Toonzone.net claimed the episode could have easily been rewritten to not include the jobbering, and I kind of agree. The only downside is that would have eliminated some of Logan's pangs of guilt about involving the X-Men. Still, no one will ever hold Logan accountable for this incident, so while it was a nice scene, I don't expect it to matter down the line.
Still, no matter how much I like the episode due to Mariko & Harada, losing to ninjas is jobbering. Has Wolverine ever lost to nameless henchmen in this show to make someone else look good? No. He came very close in "Battle Lines" for Mystique, but, to paraphrase, "close" only counts with horse-shoes and hand-grenades. There was "Badlands", but losing to a Sentinel is not as bad as losing to nameless canon fodder. Plus, now I will have a very hard time taking any threat the X-Men face and overcome seriously, when they couldn't even stop some ninjas. I mean anyone can beat ninjas. Aunt May with a broom could beat ninjas. Throw a rock in any direction in the Marvel Universe, and it hits a ninja. That's how low on the totem pole it was. It was a required story contrivance, and I liked the whole episode, but it was that one crooked sprinkle on the sundae, I guess.
"Jobbering" isn't good writing, it is the easy way out usually taken by such WAR AND PEACE style epics as DRAGON BALL Z. "Oh, my, someone pummeled Piccolo with ease, they MUST be dangerous!"

(Not to rag on DBZ fans, but high fiction it isn't.)
Still, "Code of Conduct" was better for me than some of the SIX Wolverine focused episodes, such as "Thieve's Gambit", "Wolverine vs. The Hulk" and even "Past Directions".