Secret or not, even among themselves there has to be a significant number of people with enough common sense to tell that they way they are doing things is wrong even if they believe what they are doing is justified, or so I would like to believe.
Let's say I think the oni should be eliminated, would I go out of my way to make them suffer or be an asshole to them or my subordinates? No, I would make it as fast and painless as possible. Not only is more efficient that way, it's more humane, which one would think should be a priority for the "good guys".
Even if you take the "ends justify the means" stance, their methods still come across as inefficient and unnecessarily cruel. Letting assholes take leadership roles isn't exactly great for morale or the chain of command either.
I might be forgetting some plot details at this point, but that’s how I see it.