This is basically a "It looks cool in the move so lets do it." thing. Based on everything in the comics, Adamantium once hardened is pretty much indestructible, even by something made of adamantium or similarly invincible metal (Uru (Thor's Hammer), Adamantite (Hercule's Mace)) They did a test in the Avengers where Thor, one of the physically strongest beings in the Marvel Universe, hurled his hammer at a tube made of adamantium with everything he had. It put a small, almost unperceived dent in the tube, that was it. So, by comics standards, the Samuri's sword and Wolverines claws shouldn't have been able to cut through each other, even when super-heated. But as its been noted, the films often don't follow cannon.
But I wouldn't worry too much, I doubt He'll be without his adamantium claws for long, especially with Magneto back in the picture and Brian Singer at the helm.
As a side note, there is a metal called Antarctic Vibranium, also know as anti-metal, that can pierce adamantium. if they had made the Samuri's sword out of that, there wouldn't have been any argument at all....just another indication that most filmmakers just don't care enough to do a little research. But, that's just how it is I guess.