Yes, I think perhaps we don't disagree but are defining our terms differently.
I would say that if "Scientific theories have implications that can suggest likely outcomes for certain actions" and those actions have moral status, then the scientific theories themselves have moral implications for those actions--- in other words, whether and in what respects the theory is true or false--- has implications for whether the actions taken are right or wrong.
The standard of moral judgment is, as you say, outside of science, but I would say that how we may apply that standard is constrained by science.
For instance, let's say lie detector tests are pretty unreliable. Even if I'm a prosecuting someone who's failed the test and I believe killers should be punished, I'm be constrained by the inefficacy, as proven by science, of that device.
Again, the standard--- "killers should be punished" lies, as you say, outside of science.
So even if we're putting things differently, I don't think we really disagree here.
So, with regards to eugenics, the question is, was it the moral standards of the eugenicists that were our of whack?
Or was it their understanding of Darwin, Malthus, or Galton's theories?
Like I said, I don't think this is a simple question, and most who bought into eugenics, as Teddy Roosevelt--- who, like Darwin, was a great man--- were not monsters.
But I do believe it is an important question.