I would be "all in" on Ebenezer being the bad guy except it's a bit too obvious. If it turned out that Ebezer was nemfected or even if he wasn't but decided to remove Thomas by mind whammying him into attacking Etri, I would find that to be really weak writing. Yes, it obvious that when Eb said, "Time to get to work," while he was leaving the Swarthalf compound; he hadn't given up on making Harry "see reason." Ebenezer had a plan, or at least an idea, that he was going to pursue no matter what Harry thought.
Ebenezer's idea must have involved time travel, probably to the future because changing the past is too difficult. That's why the corner hounds were so interested in him. I wouldn't be surprised if Eb gained information that might clear Thomas, but he doesn't care to do so because he was trying to save Harry from himself.
Mab would definitely have called Ebenezer an abuser; if she understood the concept, that is. I'm disappointed that Harry didn't learn from Mab and turn Eb's argument about abusers against him, the way Mab turned Harry's argument about Molly against Harry in Cold Days. It would have been quite stunning if Harry had said something like, "Abusers isolate their victims. Like I was isolated when I left in the foster system, and again when I was left to be trained by Justin and when I saved from the Council's wrath by you. Yea, I think I know all about being isolated by an abuser." Harry could have felt really guilty about saying it later, but it would have been awesome at the time he said it.