Yeah, he was, wasn't he? Was that the fair thing to do? No. It wasn't, but it was what Harry believed in and he couldn't set aside his own beliefs in order to accommodate the ideologies he was vehemently against. But the boy was genuine in the moment as far as Harry could tell. He didn't like to see kids hurt. For a moment he didn't do anything, then he crouched down so he was on level with Kvothe and could look him in the eyes, since the gaze could only be done once.
"I can teach you laws and I can show you the right thing to do, but the rest is up to you." And Harry wouldn't have been any better in that situation, maybe, with the bandits and women. He knew that, he knew the capacity for brutality and it scared him. He was afraid of the thing he could become.
"So listen to me. There's a man here, his name is Carlos Ramirez and he's a Warden of the White Council, like I am," Harry spoke slowly, but deliberately, "and in the first moment I doubt your sincerity and your commitment to being my apprentice and following my rules I will tell him you're a warlock. Do you know what a Warden's job is?" He paused. "We're meant to protect people from warlocks, and Carlos' job is to see them executed. When he has any cause on my command to doubt you, he gets to take off your head with a fancy sword and I get to watch. If you don't want that burden behind you, you need to tell me now. Otherwise you promise, and you commit. Those are the options." He needed to be afraid of the things out there, he needed to know there were things that could kill him, hurt him. That he had to follow rules and listen.