That sounds about right. I just think that this is a "We can have our cake AND eat it too" sort of deal. Because the fact that Dofllamingo had ways in which you could sympathize with him doesn't take away from the fact that he committed atrocities. THat way, I enjoyed the greater nuance that Doffy had, while people who wanted righteous catharsis still enjoyed his downfall. If we had more characters like Doflamingo (I don't really count Crocodile, he was straight up evil until he was vaguely hinted at being more nuanced like 200 chapters later, vs the points of sympathy we got from Doffy right away as his arc was in progress), I don't think the series would lose what you have.
I would like to compare it to another series, though it's a book series rather than manga. The Dresden Files. This series has a LOOOOT of bad guys, and the main character has an incredibly strong moral fiber. Because the protagonist is so concerned about being a good guy, the theme of good vs evil is never lost, so you usually get several cathartic moments of Dresden winning over the bad guys. A lot of the time, when villains try to justfy themselves to him, he basically ends the conversation with "But you killed children" or something, "so fuck you". But there are only a few bad guys whose motivations are not explored in a reasonable amount of depth or atleast given options of sympathy. It keeps them human, atleast most of them. And despite the strong moral core of the protagonist, he intensely struggles with his ability to stay good when the evil forces of the world are so strong that he has to resort to methods he doesn't want to use but has to.
I see Dresden accomplishing a lot of similar things that One Piece sets out to do regarding narrative catharsis while also maintaining a great deal of nuance to those situations. I see no reason why OP couldn't accomplish the same thing, and I don't really see how OP wouldn't be a better series for having villains like Lara Raith or Mab or Gentleman John Marcone.