Well then yeah I agree, so long as it isn't just getting rid of it for the sake of, though with some things like the dark brotherhood or a knightly order your character should follow a certain path if he wants to gain acceptance since that guild requires your character act a certain way
Yea the factions are a different thing as they can have a codex you have to keep to, not followi it word by word though. However isntead of outright kicking you out many could scold you for certain actions, demot you, give you punishments or penalties and the like.
Also bringing up the Dark Brotherhood, PLEASE don't say "they're a evil faction, they should deamnd you to do evil things" because that's just silly. Why would they demand you to do "evil stuff", even the worst mercanaries wouldn't demand you to randomly kill people or behave like a total dike just because you're a member. Anything outside the factions business isn't their business as long as it doesn't give them a bad name, the DB sure wouldn't scold you for helping out in a homeless kitchen (mostly as they're a secret organisation and people shouldn't know you're one of them, so this could possibly only help to keep cover) but something like the temple would give you hell if you got caught stealing.
And even then, even if you play in a faction that's not far off being called "the order of saints with a sword" there's still room for behavior.
All making stories here, but why not discuss the problem with video games and story. Any good writer knows that a story flows naturally, outlines are not set, and anybody who has played video games knows that most video games are not like that at all. The author of the story might be writing an as good story as ever possible, and it might be awesome, and in the writer's mind flow perfectly, but once put into a video game, it's just another cage. That's why people play open world role playing games, and that's what we're looking at. In most games, players will be annyed they have to do what the story tells them to, in RPGs, people will be annoyed because the gamemmakers didn't allow such a decision. It's limited by work, of course, so a perfect open RPG will never work unless it's a player driven MMORPG with lots and lots of possible actions.
For different possibilities, gammekers make faction or even good/evil/whatever alignments, even if it's a lot more complex, people don't like that either. A perfect story will not work in a video game, because it's an interactive story, and all actions can never be presented.
That's the reason why i suggested a http://www.gamesas.com/bgsforums/index.php?s=&showtopic=1066138&view=findpost&p=15507566