I really doubt they will kill off the real Cap and have The Winter Soldier take his place. It does happen in the comics, but that doesn't mean it will happen in the movies. Marvel signs everyone to at least 8-9 picture deals now, because they don't want to go through what happened with RDJ ever again. Just because it's a nine picture deal doesn't mean they have nine movies planned, it just means that if they want to use his character again, he will be obligated to come.
Even though it's a nod to the comic book fans, you have to remember that most of the audience who see the movies aren't into the comics. So for the same reason you won't see Ben Reilly or Miles Morales as Spider-Man, Dick Grayson or Terry McGinnes as Batman, I don't think you will see Bucky as Cap America. Steve Rogers is Captain America, and killing him off would just be stupid. Besides, I would imagine after the third Cap America movie, Marvel will "shelve" the character for a while. They have other heroes and characters they haven't explored yet, and we know a Dr. Strange movie and a Black Panther movie is being planned so. I would also imagine a sequel to Guardians of the Galaxy will happen, and a sequel to Ant-Man might not be impossible either, depending on how they do ofc.