There is still a way for Microsoft to release Goldeneye on the 360. All they would need to do is remove any signs of the James Bond name and change the character likeness; then they could release it under another name. The only stake that Nintendo could ever claim in the game is that they published it and that they paid for the Goldeneye license which Rare used on the N64. Rare own the actual level designs (which is why they are included in Perfect Dark), so if they made the changes I don't see any reason why they couldn't release it. I would have thought that they could have pushed for the entire game too, but it probably would have cost a lot, more than they would make in profit (PD got pretty poor sales on 360 despite people claiming it was where 'all the fans had gone'). Ergo, Microsoft didn't see enough $'s floating around to pursue it further. Not that they had too much interest to start with, as they did say that Goldeneye wasn't the type of game they wanted on Live back in 2006.
Must be great for Activision though. All they had to do was sit back and wait for the big N or MS to come calling with a big cheque and pow!, there's the exclusive Goldeneye remake.
If anyone is really distraught over the Goldeneye remake there is an easy quick fix for you. Go buy Perfect Dark on the 360, it features some of the multiplayer levels from Goldeneye, so you can get a taste of the original there (kind of).