I agree with the amoral assessment of Vegapunk. I mean, certainly he has done good things, because of what he has done for Baldimore, but I would hardly qualify "letting Kuma program one final mission of his own" to be noble. To me, the entirety of what Vegapunk has done to Kuma is immoral, as he has essentially killed the man by taking away his humanity. Even if Kuma has done it willingly (and here the definition of willingly seems to be called into question as well) that kind of experiment still raises all sorts of moral questions.
Basically, my opinions is that if Vegapunk was inherently evil, I don't believe he would have made the positive progress he has in the field. If he felt loyalty to the marines, he would not have allowed Kuma the final mission that he gave him. If he was inherently good, he would not have created the Pacifista project.
So I agree with the amoral assessment. This obviously isn't a perfect analogy, but I would say Vegapunk just wants to pursue science like Luffy wants to pursue One Piece. If he helps some people along the way, awesome, good for them. But he's not looking to be a hero, nor to cause any serious damage. He just wants knowledge.
I suppose the alternative to this was he began as inherently good, and then the World Government pressured him into using his knowledge for other things. But I suppose the most likely option is something more ridiculous than any of us can imagine, and no one will see it coming.