So you literally don't know what you're talking about. The Scorpion Clan Coup and them being removed from the game wasn't due to a player decision, that's literally how the game started - with 6 great clans. The first Scorpion stronghold (The Ruined Fortress of the Scorpion) was in Shadowlands, the first expansion. Not a player choice. Two years later, when the story and game did a flashback, and the actual Scorpion Clan Coup set was released, the Scorpion Clan continued to get cards printed as normal. I guess you could be actually referring to when Toturi exiled the Scorpion, however that wasn't a player choice or storyline result either.
The Spider, as noted, continued to function as a clan in game, and ended up with a better story because of it. That's basically what AEG had said beforehand would happen to whomever lost that mega-game.
In none of these situations was a clan removed from playability due to an event.