Ok I've done some more thinking how about scrap my original idea about how the town starts. How about you are approached by a guard in falkreath alerting you to a nasty werewolf responsible for the murder of several travelers on the road and you are tasked to hunt him down and kill him, after tracking him and finding him in a cave he confronts you in human form warning you to leave the cave or he will be forced to kill you to keep his location a secret. Realizing that a savage werewolf wouldn't warn you before attacking, you try to get the full story about the attacks. he tells you that the attacks are not from him but from the silver hand that seek to eradicate him and his family by trying to get the town guard to go out and hunt his family down.
I know you might say why would they go through that trouble when they can just do it themselves why would the town guard go out and hunt something that hasn't caused harm to the village? If the silver hand are caught slaughtering a family that no one knows are werewolves then they would in turn be hunted.
So you decide to help the man hunt down the silver hand hunting party and after killing them you learn they are but a small fraction of a bigger force, you are then asked to help him get his family and help them find safety which leads to you finding an abandoned meadhall in northern falkreath where you start the foundations of a safe haven for werewolves.
Perhaps after getting the man and his family to the meadhall he suggest building a community for those who are in the same position as he and his family are in, more werewolves and people sympathetic to the cause would help fend off the silver hand hunting parties. You could go out into the world and find feral werewolves and show them how to tame their beast, seek out non werewolf settlers and refugees to move to the village to help make it seem like just a normal hunting village. I could also make it so you have to fend off attacks from the silverhand and go on missions to destroy their organization.
I think this would be a good idea, would be hard but would make a great mod.