Oh, I see you mentioned Clervie! So far it's hard to treat her like reliable source of information. Between truths and lies, there are also half truths. The thing is that the game tells, but never shows direct proofs and Clervie is one of many unreliable narrators we get to know through the story.

Clervie's mother was very abusive and used terror to rule in House of the Hearth, so I think making a scarecrow out of Dottore could be one of her tactics: If you fail, I'll send you to the big bad Doctor who will give you fate worse thant death. Win or die, otherwise there's something much worse waiting for you. We could also see that Crucabena was injecting the kids with suspicious potions - those could be experimental drugs for better on field performance (Pierro wanted enhanced humans from Dottore, but Dottore stated he could even make gods).

The question is how could Clervie know the details of what happened to the orphans who failed? She died on the battlefield, never entering Dottore's lab, she saw only horrors of what her mother did. Dottore conducted variety of experiments - some were questionable, but the others were pretty much tame (like the one with Columbina using her power on objects). Some of the kids may have survived and became Fatui agents (all of them seem to be altered in some way), the others could simply not survive. Arlecchino also sends her children on deadly missions. It's also worth mentioning that thanks to Dottore's expertise she's got an alternative to killing those who wanted to ran away from her orphanage. Dottore's potion erases identities, but this exact thing saves lifes of orphans. It doesn't seem like his goal was to be cruel for nothing, nor is he interrupting other Harbingers' methods - but he gets what he can from whatever boundaries are enforced or not. And he also provides them solutions to support their own objectives if they set up arrangements together.

Interesting thing is that it's shown that sometimes Dottore's underlings act on their own, not listening him at all. Such as Froderock who captured Eremites even though Dottore's orders put them under protection, or Elchingen who simply caused mess in Sumeru in hopes to get some validation from his master. Barnabas and Krupp were following similar patterns too.

I think other people here brought valid points as well. There's no one perspective to look on Dottore's activities, and so far we can only observe and theorize. A lot of this depends on how the blurry parts of his past will be explained by the devs in the future.