Nah, I don't buy it. They are all evil bitches deep down, some just make excuses for it. As you pointed out, Veronica does some shady experiments with prisoners, but the thing is, what she does is not science, it's cruelty masquerading as science. She's "Mengele-light" in a hot ginger body and, admittedly, much more knowledgeable and intelligent. Which makes it even worse, because she IS smart and absolutely COULD find more humane ways to conduct her experiments, but CHOOSES not to do it. She literally made her servants deaf and the game (through Elena) even makes a point about that. Man, the more I think about it, the less sympathy she gets.
Yes, it would be foolish to kill her, because she can potentially help save the world, but I think she's already proven that she doesn't deserve the power she has. I would try to convince her to do some good, but always keep her on a short leash.