In part this is arguing over a definition of nature.
You're going for the obvious "We are part of nature because nature created us and we work within the system." while they're going for the idea of it being more strictly influenced by evolutionary change which we have the ability to 'escape' (escape in the sense that we can go farther than an animal can due to being able to design larger systems without having each step useful).
The definition of "we are of Nature" is essentially "we are of Physics". This is true, but its not really useful.
On your morality lines:
Morality is a personal concept in people, but it is influenced by society and the people they interact with. There doesn't have to be some objective right/wrong, and so people can say that the scientists were being immoral (according to the person's own moral ideas).
The scientists may very well believe they were being moral, or perhaps they didn't think about it (people do that!)
> that our nature-created brains have led us to create?
Well, as stated before, morality isn't the same between humans. There's no objective authority that decides X is right or Y is wrong, simply social/cultural influences throughout the world.
You could view morality as a way that you think the world/people should behave to maximize some value you hold. Perhaps you value sentient life, and so you hold self-sacrifice to save a dozen people to be a moral good as it continues more sentient life.