My question for Eb/Thomas is less about motivation and more on terms of tactics. So Eb could be warning Harry that it's
doing the backstabbing, which would mean that's it just that Thomas is a means to and end and/or bonus of getting someone harmful out of Harry's life? So this warning is for Harry to have a way to figure out its Eb, who's more or less under duress and wants to give Harry an opportunity to either give himself an out and/or expose parts of the Council.
Maybe Eb has been given false info about Thomas or the circles he moves in and due to his bad experiences and biases, he doesn't look further b/c Thomas.
So maybe the Black Council/Nemesis wants to separate Harry and Thomas as well. That way, they can fully destabilize Harry and Thomas is just the first of Harry's allies. So it's almost like 'White Night' again. (Though I can see this going out of control for them.) Maybe that's how we see Cowl and possibly Kumori again, b/c the former has experience with the WCV.