There is a Sega of Korea, and there is currently no word as to why the Korean division will not be handling the game.
This, however, isn't the first time Nintendo has published a Sega title. Mario and Sonic at the Olympic Games was published in Japan by Nintendo while Sega of America published it in North America. Also, Sonic the Hedgehog appeared in Nintendo's Super Smash Bros. Brawl last year.