So... Did I miss some important pieces of the questline, or does it go from "casual investigation" to "Burn everything and kill everybody, let god sort them out" in the blink of an eye?

Things seemed to be progressing at a normal pace, I'm getting some background on everybody here, some things seem a bit fishy... Then all of a sudden I kill the Salamandria boss and the mob is trying to kill Abigail.

That doll looked like Odo? He killed his brother? She made him do it? Somebody was raped and killed herself?

EVERYBODY DIES!

Kill the Beast. Who summoned it? Anybody in particular, or just the fucked up evilness in general?

Was Abigail a nice lady or the devil incarnate? Is it answered?

Why did she sleep with me as I was escorting children out of a cave? Thanks, but a bit inappropes maybe?

Why is every last person in this village dead now? Why are their corpses left laying around?

What did I miss?

What do you missed? you did not pay attention to side stories...

I was trying to, but it's like it just jumped ahead to the end of everything.

I have no clue who the raped girl is.

I saw the doll in Abigail's hut, but absolutely nothing hinted that it looked like an NPC, much less that she was (or was not) controlling him to kill his brother.

I had a lot of the village left to explore, I had sidequests left to complete.

All of a sudden everything's at the conclusion and everybody's dead.

Why are the villagers dead?

I know that the Beast was created by somebody skinning a puppy or something like that, but who? Why?

Well, reload a save game before you choose to talk about Salamandra with the priest, and try to finish all side quests, you will gain story+xp+money...