Nintendo has no such rights to 3rd party content.
They also published a variety of other projects like the Banjo games and Perfect Dark. So merely being the publisher doesn't mean that they hold any rights.
The most common and believable story that I've seen with Goldeneye basically goes as follows. Rare wanted to remaster this for XBLA and was in the early stages of the project with the sticking point before proceeding past a proof of concept demo being securing permission to utilize the James Bond license. Rare pursued this and contacted the videogame rights holder at the time, which as I recall was Activision.
Activision agreed to assist in getting this back out there with the condition, in order to protect their relationship with Nintendo, that Nintendo unofficially agree to this since Activision didn't want to ruffle any feathers with their relationship with Nintendo by assisting in getting a classic so closely associated with Nintendo onto the competitor's platform. But sadly, Nintendo told them that they'd prefer if it didn't happen.
Rare supposedly even offered to allow the N64 classic to appear on the Wii's Virtual Console service if they agreed, to no avail. So silently it sits while other original Rare creations from the N64 that were published by Nintendo have been remastered (Conker on the Xbox and both Banjo games and Perfect Dark on the 360).