Vegapunk was the chief researcher from a facility that undertook experiments on minorities like Arbel
Vegapunk was not in charge of those experiments, Ceasar was.
And the Seraphim don't have a conscience, Oda clearly showed that. They are machines. Their behaviors are automatizations. They don't have """free will""" and they do not think.
Trust me, before defending Vegapunk, I made sure of that, because at the beginning of the Arc, I was not liking the guys. But since the Seraphim never displayed any form of conscious behavior (and no, little Hancock being surprised or shy is not a conscious behavior but an automatization due to her Hancock lineage) you can relax on this.
Vegapunk never did something very problematic. At least that's what I remember from the story, maybe I missed something.
But EVEN if it was the case, I did not say I agree with the guy. I think his lack of care for his action is very problematic and a symptom of people who play with scientific fire. I'm not defending him, I'm saying that this is a very interesting character.
Don't put moral into this. You can find a monster interesting and it has nothing to do with sharing his values.
But in this case, I see no reasons to really blame Vegapunk aside the fact that he his flawed like many humans.