It's been a while since I ran it, but I remember the main threat was the spider cult when my players played. One of them got tricked into entering the location of the spider alone, and it was a high level spider so it infected that PC pretty quickly. The other players did not know this PC was infected, so then I told that player the only way they could gain XP was by furthering the goals of the spider cult. They then tried to trick more players into going into the location of the spider alone (and managed to infect 1 or 2 more PCs, I think...)
In my sessions there was no real threat from the Duvan'Ku cult in Scenic Dunnsmouth as that was something that happened long ago and even the villagers weren't really caught up in it any more. I think Uncle Ivan was the main physical threat to the players, and I think Magda was part of the spider cult and responsible for getting that first player infected.
Getting infected by the spider sucks, so I wouldn't necessarily change things to make it harder for the players. But the villagers could use overwhelming force if the party shows their hand (ie, they realize there's a spider cult) or they could use a divide and conquer strategy if the PCs are foolish enough to investigate areas alone.