It's a bit disingenuous to say that Nintendo got into a dispute about re-releasing it. The original game was developed by Rare and published by Nintendo. Since the original game, the rights to produce Bond games passed to EA and then to Activision, neither of whom wanted to publish any Bond games for some time as they didn't think they were profitable. Around the same time, Microsoft bought Rare and, by extension, the IP of the original game. So, there were conflicts over which system it should be published on based on who originally published it (Nintendo), who held the rights to the game now (Microsoft via Rare), and who held the rights to produce new Bond games (EA/Activision).
It's been a mess, basically.