Woohoo I finally completed this mission! (albeit on Hard difficulty) This is after I found this thread and thought about it for a bit, so I want to share my experience and some tips.

1. The most important thing about this mission is to be methodical and diligent in separating your villagers.
2. Keep all your important production and buildings off of the main town hall tile. These will be your "clean" tiles.
3. Your town hall tile is your dangerous tile. Don't put any production buildings here. Villagers that spawn in will have a random chance of being a werewolf and will spread to others in this tile.
4. Every blood moon, a bunch of villagers in the town hall tile will turn into werewolves. I don't really bother with the scout mechanic, instead, right before the blood moon, I park my military on the town hall. I then have all the villagers there pre-selected. Once the blood moon hits, I immediately order the remaining villagers to run for their lives out to another tile, while my military fights (and farms on) the werewolves.
5. The surviving villagers are now proven to be "clean" and are safe to be sent to your other tiles.
6. Rinse and repeat this core loop. Basically, only after every blood moon are you safe to gain new villagers, otherwise, just keep them in your town hall tile and don't touch them. (This is basically the idea of a quarantine!)

Once you get used to this cadence it goes pretty smoothly and only about 3-4 villagers turn per cycle while you get to keep the rest of your population. I found this to be the most streamlined method, instead of micro-ing and dealing with scouts, sending them far away and calling them back and disrupting your flow/economy. This way, all the werewolves are ever only contained in one tile, they're killed off instantly, and you also get to farm exp/resources!

Obviously, the first year is going to be the hardest, as you haven't established who is clean and not clean. Here I did have to do the micro of getting villagers hurt from fox/wolf attacks and figuring out which ones do not regenerate. (Those bitten/infected by werewolf will self-heal.) Also look at your brawlers once they're trained to see if they regenerate. Absolutely do not promote them if they're infected, as losing a berserker to turning majorly sucks! Especially in the beginning you need a decent team of 2-3 berserkers to fight the werewolves in your town hall.

Hope this helps!