The film was an expression of Bergman's crisis of faith. Like many other films, westerns for example, it takes place in the past, but deals with the present. The crusades can be seen as the 20th century holocaust, while the plague, and the fear it caused, is clearly the Cold War era possibility of nuclear destruction. Bergman, who was raised in a religious atmosphere, could reconcile modern reality with an existence of God.
As for the questions:
The scene in the inn has nothing to do with religion, but with how people are happy to enjoy another's pain and humiliation, especially when it gives them a few moments of relief from the fears. The scene also strengthens the side of Jöns character, that with all his cynicism, he's the one to acts, when it is necessary.
Skat is dead, because, as noted above, Death made it so. It's also a moment for some humor, as are other scenes with Skat.
I don't understand the next question.
It was common during periods of plague, or other traumatic eras, to find scape-goats, usually women, Jews, Gypsies, or others. She might have been an eccentric young girl, which made it easy to single her out. When Blok asks about the devil, and mentions the horror in her eyes, she says, more or less, that that is the devil, and she sees nothing but emptiness.
While we can't KNOW what a character felt, I think that Bergman allowed him to die without finding the grace he looked for. The only moment of grace he had in the film was partaking in the milk and wild berries with the (holy) family. There's nothing more than that. God can not exist in the same universe in which a holocaust exists. This is the crisis in faith that Bergman was expressing.
I want to shake every limb in the Garden of Eden
and make every lover the love of my life
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