I don't see the nature of the game being particularly relevant. A decision to give a videogame character a final "death," whether the character is from a game with a more or less complex story, or even whether the character continues from one game to another, is fairly arbitrary. Most games fall on a scale of being more story than gameplay driven, but to me, Metal Gear was always about "Tactical Espionage Action" with a story tacked on around that, not the other way around, so I think your distinction is murky. Samus or Ryu could be "killed" and fail to show up in subsequent games (there is a kind of story underlining Street Fighter and Metroid games, after all), or not. Same goes for the guy from Uncharted, Snake, Final Fantasy characters, etc. So my question is--why does Solid Snake specifically need to die while others don't?
But in any case, a huge chunk of games out there (most of them?) are either sequels, prequels, spinoffs, or extremely derivative takes on existing, popular games. Metal Gear's story was pretty bat-____ nuts from, at least, MGS 1 on, to varying degrees, so I don't think they have reached a point where Kojima has gone "too far." If there was such a point, surely he pushed way freakin' past that with MGS2. There are so many options and possibilities for exploring different characters and different previous stories, that I don't see why it is that much worse to continue on with the franchise until something truly horribly bad comes out and he proves that he isn't capable of producing a good, enjoyable game anymore. MGS4 was awesome, and had a nice feeling of finality to Snake's story. But that doesn't mean that there aren't other great games from that universe that Kojima can explore.