Harry is letting Thomas around Maggie unsupervised.
Y'know, the girl named for Eb's own daughter?
Thomas is defiant and comfortable in Harry's home.
I think Eb's supposed to have been *stewing* about Thomas and whatever "hold" he had on Harry. He may have had a similar confrontation with his Maggie, and she chose Papa Raith. Now here's Harry doing the same.
From Eb's perspective: Harry has, in this book and Changes, tossed in his face a "Let the world burn, then!" attitude when it comes to family. His defiant comments about the foster system initially would have seemed to be purely about his daughter. Eb, an old and wise man who cares deeply about Harry, realizes that Harry is including Thomas, *similarly abandoned by their shared mother*, under that defensive blind spot. Harry will choose Thomas over the Council, and the consequences be damned.