Quite early in the story, Eb shows up at Harry's apartment (having disrespected the svaltalve's security in the process). There he discovers 1) that damn vampire hanging out at Harry's as if he's part of the family, 2) Thomas apparently is accepted by the svaltalves enough to be allowed to wander without a security escort (proven when Thomas leaves without issue), and 3) little Maggie is not only living there, but Harry seemed perfectly comfortable having THAT particular vampire around his girl...Eb's great-grandaughter, named for his own daughter.

Eb tries to convince Harry that all of this is a bad idea. Living in the svaltalf stronghold ("You idiot," Ebenezer said through clenched teeth. "Do you know what these hosts of yours are capable of?").

The pitfalls of trusting a White Court vampire ("...you’re young, and I got experiences with them and perspective on them that you don’t. I don’t want you to figure it out the hard way, that’s all.”).

About allowing Thomas near Maggie (“You let the vampire around her?” my grandfather whispered, his expression shocked).

And most importantly, about Maggie's presence in Harry's life (“You might as well get her a shirt with a series of bull’s-eyes on it,” he said. He kept his voice pitched too low for the children to hear him. “You raise that child near you, and you’re making her a target. My God, the vampires already know about her.”)

At this point even Harry can see that Ebenezer is ready to take drastic action. “I think that right now you’re considering protecting her by grabbing her and stashing her somewhere safe. If you go through with it, I’m going to take her back. Over your dead body if necessary, sir.”

So Ebenezer gets to plotting. How to get all these dangers away from Maggie? He can't remove Maggie without a fight.

So he comes up with a plot...use magic to invade Thomas's mind, to compell him to assassinate Etri! He's the Blackstaff, after all - he's allowed to break the Laws of Magic. But make sure he's also compelled to 1) damage the building, and 2) get captured, to be sentenced during the peace talks.

This solves many problems, Eb thinks. Harry will see that all WC vampires can't be trusted. Harry will lose faith in the svaltarves, either because their security was breached, or because they beat his friend, or because they demand Thomas's head during the Accords gathering. The burning building will encourage Harry to move Maggie to a safer place - the Carpenter's angel-warded home (which only protects from supernatural threats, so theoretically he could still snatch Maggie if needed).

Of course, Eb needs to keep Harry from going off the rails. So he shows up outside Justine's apartment, harping on the twin themes of Thomas = bad, and Harry Maggie = danger for Maggie. He keeps pressing and pushing at Harry, and even the appearance of the corner hounds doesn't make him quit rehashing the subject.

And when Harry defies him, rescuing Thomas, Eb snaps. The only thing he can figure is that the White Court has something on Harry. He fights with him, then begs Harry to tell him the truth.

“What do they have on you? It can’t be so bad that I can’t help you get out of it.” His eyes softened for just a second. “Talk to me.”

“They don’t have anything on me.”

“Then why?” he demanded. The calm in his voice was fraying. “Why are you doing this? Why are you destroying yourself for that thing?”

And when Ebenezer finally learns the truth - he has a second grandson - he realizes just exactly what he did in mind-fucking Thomas into an assassination. He literally condemned his own grandson to torture and death.

Ever had a traumatic event happen, and found your mind focused on only one small aspect of it, instead of trying to process it all at once? Because all of it, all at once, would be so overwhelmingly awful that you would go mad?

That's where Eb was at that moment. He couldn't focus on Thomas, because that would mean he'd have to face his own actions in a new light. So he focuses on the only thing he can, the only thing that paints someone other than him as the bad guy. "...that pig, Raith . . . with my daughter....”

tl;dr Ebenezer put a mind-control whammy on Thomas to make him attack the svartalves, because he thought Harry and Thomas were too chummy, and that Thomas was endangering Maggie, too.