I'm pretty sure Justine made him do it. With the proviso that I'm not certain if what we see is really Justine and that I don't know if was some form of mind control or just blackmail. Thomas keeps saying her name as a warning.
I also strongly feel that Justine is behind/in on it.
1) Eb makes a big deal about someone stabbing Harry in the back.
2) Someone is leaking information from the White Court.
3) Niall001's last sentence is a credible interpretation, especially within the context I provide below.
4) All the interest in Justine. She's more important than just Thomas's baby mama.
Counterpoint:
For one thing, I'm not convinced Thomas was trying to say "Justine".
Thomas never said Justine. I think the quote is "Justin-" and "J". Harry responds he's going to look out or take care of or already has taken care of Justine both times. Thomas responds with sobs or something similar both times. If it was Justin Dumorne, then mind magic and an f-you to Harry is a good explanation for why Thomas did it.
We really don't have any suggestion as to why Thomas did it other than someone threatening Justine. Harry does hint that maybe Thomas failing to kill Etri was intentional. We also don't have anything in this book as to why someone was trying to kill Etri.