Popular thought would seem to state so, yes.
But there's always the chance that somebody will say, "why don't we try something different?" Human beings been known to do that sometimes, and whether corporations are people (they aren't) or not, they are in fact run by people, and sometimes those people do crazy things that become wildly successful.
The making of Chrono Trigger is a good example; Square and Enix don't seem to have wasted much time, they just called each other one day and said "what would happen if we got our teams together for a game making party?" The result was a huge freaking hit, and still inspiring people to this day. Hard to top Chrono Trigger. And it was just a whim, you know? They didn't sit down at marketing meetings and say "let's team up with a rival company and make a game." Marketing would have shot that stuff down.
Nintendo has options at this point, they could C&D development of the game itself, or they can own this fan game and make a lot of people happy instead of going around pew pewing everything their fans like with their NES Zapper guns.