That's not what we see when Eb is on-screen, and it's not what we see in how other people react to Eb, and it's especially not what we see in Peace Talks.
Every book where Eb is on-screen, we learn that he's not at all who Harry thought he was. In Summer Knight we learn that the irascible hermit is politically connected enough to swing a Senior Council vote. In Blood Rites we learn that the "magic is not for killing" sensei is actually the White Council's dirty-jobs assassin. In Changes we see him ripping the life out of humans, just shredding the first law and everything he's taught Harry.
And Harry's still isolated -- which we're told in the text is "what abusers do". After years of living with Eb, and years of living after that, he doesn't have a single wizard friend until Luccio drags him into the Wardens and he meets Carlos. That made some sense when we thought Eb was a loner hermit, not so much now that we know he's a political mover and shaker with lots of wizard friends.
What are the big fights about in Peace Talks? Eb wants Harry to cut himself off from Maggie -- to whom he says exactly four words, upon first meeting his great-granddaughter, before disengaging from her completely to have a knock-down-drag-out fight with Harry insisting that he has to send her away.
The other is about the White Court Vamps -- but is that really about protecting Harry from them, or about a predator marking his territory? If Eb does use subtle mind-control magic, he might worry that WCVs would be able to spot it in Harry. Could he have been freaking out about Thomas because he thought Thomas could expose him? (Did he arrange Thomas's death for that reason, and to isolate Harry from both the Whampires and the Svartalves?)
WARNING: The following paragraph is kind of jumbled.
The "Ebenezer is behind Thomas' actions" theory is a compelling one, especially when one looks at ALL the different theories out there and compiles the various pieces of evidence different people present. But, I don't think Ebenezer is or was purposefully trying to isolate Harry... in the early days. They have two VERY different approaches to life as a result of their histories. I suspect that is the driving force behind their disagreements up until Peace Talks. Now, I am firmly in the "Ebenezer is Nemfected" camp(along with Gedwig from Svartalf security, but we aren't talking about that right now). I won't go into the "why" I think this. There are so many theories out there that it's not hard to dig up half-a-dozen reasons it could be the case, or even a dozen. If that counts as Eb trying to isolate Harry, meh. I'm not sure it does, though. The possibility of an Obadiah Stane "Who do you think locked you out?" line is quite possible next book.
And then there's the cornerhounds... we see Eb getting Harry to do two things which are explicitly Warlock-bad things: using a ring of fire and making direct mental contact with the Outside. We only have Eb's word, in a vague and shifty fashion, that the latter is actually safe for Harry. And the former seemed like an unnecessary risk.
And imagine what that scene looks like to a White Council that's thinking about kicking Harry out, again.
THIS! THIS! The "oh, and this is what a Starborn is" exposition seemed so out of place that it was almost jarring. A reveal like that seems like it would be something more suited to a climactic battle or high point during a book.
Anyway... if we imagine that Ebenezar McCoy was Peabody's boss and has been trying to isolate and mold Harry into his tool, a lot of these things make sense.
Now, this I don't believe for a moment. If this were true, Eb could have just
not done anything during the mistfiend incident, or more effectively he could have started throwing power around AT THE OTHER WIZARDS IN THE ROOM. As the heavy-weight, bestestest fighting wizard on the planet there would have been a ton more deaths, and the white council could have either been crippled or undergone began a civil war while they were already occupied with the Reds. The outcome, no matter what happened, would have been absolutely
DEVISTATING.
Eb trying to mold Harry is quite possible, though. Into what, though, is an important question.
However what Eb himself does is represented in the real world by paramilitary police death squads. Murderers above the law. I don't really get the urge to give Harry the Black Staff given that, but whatever.
To be fair, Harry and Eb are already in the same line of work. They just have different bosses, and Eb has a LOT more experience.