HM interesting question! its p vague how much of his deception was deliberate but i like to think he 100% knew what he was doing setting puppeteer up the way he did, knowing what it would do to her just so the bureau can have her research to themselves. I don't think he'd allow himself to feel regret over it, and probably justifies to himself that it was necessary (it wasnt). i think the only time he'll actually start questioning his actions/choices back then is when the events of coa 4 takes place and he's forced to watch everything he sacrificed tracy's work for become meaningless, bc the results of her and pickman's research (molten hound) can't be controlled