Being barred from joining the Companions is fine, though I hope you keep an open mind about players being werewolves. A werewolf hunting werewolves would open up a number of interesting character possibilities, and there will no doubt be mods that add "normal" lycanthropy (that you get by being infected by wild werewolves, without touching the Companions quest line). Obviously the Silver Hand wouldn't tolerate it if they found out, but if a player can hide it, it would add a nice dynamic to the quests. Perhaps they could also offer a cure... once you get high enough in rank that they wouldn't just as soon lock you up for experiments/torture.
But how to implement it with Skyrim werewolves? Unless you do something stupid (on the level of turning in front of them) there is no way for them to detect the curse. Unless they have a spell/relic/whatever which allows it - but then, why wouldn't they use it on every recruit?
I could definitely see other members not knowing they have some vampires in their ranks.
Meh, I'd say they should be "pure" - to show how bad can normal humans get (which gets us to the question of who is the true monster - the honorable werewolves or the human slayers who will do just about anything...).
I'm thinking more of a cross between the thief's guild, the fighter's guild and the dark brotherhood. Violent mercenary thugs and monster hunters that work only for money and pleasure, and don't give one whit about honor or have an qualms about using underhanded tactics like sneaking into another guild's hall and assassinating their leader.
This is definately the guild I'd like to see - especcially if it doesn't involve shining armor and white clothes
You know, something just occured to me, if the Silver Hand know that the Companions are werewolfs and hate them so much, why don't they go around telling everyone else their secret? Being a werewolf is a crime in Skyrim, so they could probably cause the Companions a great deal of trouble by blowing their cover, maybe even whip up some public support against them. Then again, the silver hand might be so hated themselves that no one would listen to them or take them seriously.
Well, they'd need some proof - and a really good one (the Companions have quite a reputation, and Kodlak is respected by most of the population...