From Wikipedia: http://en.wikipedia.org/wiki/Rare_(company)
Up from the end of 2000, people from Activision and Microsoft visited Rare. In November 2001, Microsoft trademarked the name It's Mr. Pants, the name of a game which was released three years later. In September 2002, the Stamper brothers sold their 51% interest in Rare to Microsoft; following this, Nintendo sold their 49% stake in the company as well. Microsoft paid a total of $377 million for the company. Because of this, Rare is now a first-party developer for Microsoft's Xbox and its successors. This left Donkey Kong Racing, which was due to be released for the Nintendo GameCube, unreleased, though how much more had been completed of the game than the pre-released video is not in the public domain. The trademarks of the characters from the games that Rare made for Nintendo consoles (such as Conker of Conker's Bad Fur Day and Banjo from the Banjo-Kazooie series) were retained by Rare (apart from intellectual properties originally developed by Nintendo, i.e. Donkey Kong and Star Fox). Despite the acquisition, Rare still developed games for Game Boy Advance, and now develops for the Nintendo DS, as Microsoft is currently not participating in the hand-held video game console market. Rare has never developed for Sony platforms.
Basically, since the game is an original Rare IP and Microsoft owns Rare, there is no problem with it going on XBLA -- though it will be funny that it seems the N64 logo will be present.
Bond was a license owned by Nintendo and not a Rare IP. That is how Nintendo could quash that apparently. Of course, why Rare doesn't substitute the graphics and make a Perfect Dark game out of it is beyond me.
Mike from Morgantown