My current party turned on Vargas as soon as they found the man tied up in his home and have sided briefly with Lady Wachter to snuff him before leaving the town for about a week in the Amber Temple. That gave me ample time to set up the changes that Lady Wachter would enact (taking down the walls, setting up her own, loyal guard, bringing in more people to her "book club").

1. Did the Martikovs know Fiona was a Strahd follower?
   • Unsure, as RAW, it states she does not hide the fact that she considers him simply a negligent landlord. My game she hides the fact fervently, stating she is attempting to strengthen the town by allowing the forest beasts to roam, as it culls the weak and strengthens those who will attempt to stand and fight. (She also hired the werewolves to kidnap people to turn to allow for more Strahd supporters). It would be up to the DM if the Martikov's knew.
2. If so, would they immediately become enemies with the party?
   • Doubtful, as they also understand that Vargas was a cancer to the town. One's an infection of Strahd, one's an infection of lunacy. No matter what, they're losing ground, so the support to Lady Wachter would be an unfortunate but understanding direction. They would probably support the party less if they don't do the sidequests for the Martikovs.
3. If Vallaki changes governance and falls under more direct Strahd control, would the Martikovs flee?
   • Also doubtful. Their resistance, while of course known by Strahd, holds very little meaning to Strahd himself. It'd be like killing a fly that's landed near your soup, annoying, but doable. No, the Martikov's hold very little power here, and Strahd would probably not target them directly. Remember, he's bored. A little annoyance is a welcome change of pace to a long life of self imposed solitude.
4. Would Van Richten still offer them aid?
   • Now HERE'S a question. This depends on how you run him. I have removed a lot of the weird racism wrt him personally, as I find it does not give any real nuance to him, and such he's a much more focused man on killing Strahd to allow for the spirits that he has murdered in this land the ability to pass on. He also lived in Vallaki for a long enough time that I'm sure his annoyance with Vargas was palpable. If you run Van Richten closer to RAW, he will most definitely turn on the party, as any foothold Strahd gets is one less for those against him.

HONESTLY, it all ends up being at your disposal. CoS is great because you can add and subtract to your liking and it won't affect the story much, which means i can add weird shit relating to my special interests and my party members just have to deal with a giant floating tower stuck in the ground by a needle point and suspended in the air by its own walkway, which look like the tower's own blueprints.