I'm not sure Thomas was set up at all.
Right at the start of the book, there's all this stuff about how his life is about to change, how the kid is important, and how Justine has a 50:50 chance of making it through the pregnancy. Thomas straight up says he has a solution in mind for all this in the first chapter and doesn't elaborate.
I think Thomas has Made A Deal, and that cost of that deal is the death of Etri. My favorite for the culprit is Etri's sister, Evanna, who Thomas has been "visiting". I think she offered him some sort of arcane help with Justine's delivery if he'd get rid of her brother, making her the outright leader of the people. We keep on being told how amazing the Svartalves are, and how even the Norse gods didn't want to tangle with them.
The counter-argument to this is that she plays a blinder of a part when Dresden turns up, and she could have implicated him easily, which probably would have made her less likely to come under suspicion herself. Perhaps she thinks she's so in-charge of the situation that she's not vulnerable and didn't want to complicate things. I guess we'll see.
The corollary of this is that “Junghg. S’Jnngh.” could be one of two things, a real plea to look after Justine (possible, but I think unlikely) or nothing to do with Justine and a warning of something - either way I don't think it's a warning to Harry that Justine betrayed him, though I realise I'm very much in a minority here
(I think it's supposed to look like "Justine. It's Justine" and the tear falling is supposed to be love-lost, but I still think Jim is misleading us).