Doing good for your people is generally regarded as moral. Helping them, taking care of them, putting their safety and happiness above yours. Who you consider as "your people", that's up to you. If it's "all living beings", genocide is amoral. If it's a smaller group, killing people outside of it would not be seen as amoral, or at least less so.
Whether the end justifies the means, that's a good question. Does it depend on the means and the end? Was killing Orlesian chevaliers to free Ferelden good? If the warden kills a guard who's just doing his job to infiltrate a mansion, is it an evil action? If someone kills a friend or a family member, would it be evil to kill them too? When something is personal, people stop caring about the reasons behind actions. To put it coldly, there's a conflict of interest. If I were a human in the scenario you presented I would try to stop that elf, and probably end up doing some questionable things in the process. But I don't know if I would call that "good".
Morality is a dodgy and complex subject. I still don't have a defined opinion about it. My current take is what I wrote earlier: "From a philosophical point of view, I'd say evil people don't exist. Everyone is merely the product of their life experiences, and their own reactions are derived from these experiences too. From a practical point of view, there's a point where you have to draw a line, stop thinking about people's abusive childhood and plant a bullet in their head."
I don't think tribal definitions of social groups - in any modern moral theory - are really taken seriously anymore. While there are views (and people) that might argue that it's difficult to say that someone is "evil" if there is some very culture specific morality that they are adhering to (within reason), e.g. if there is a culture that's discriminatory (e.g. US in the 1930s) not very many scholars would argue that people in that society were evil for discriminating. But at the same time there's a huge moral difference between withholding a benefit and actively inflicting harm.
And my question wasn't about ends justifying the means, though that's a thorny debate. It's that people intend ends as much as they intend their means, and if the standard for morality is "intention", then we have a serious problem about which intention we actually say counts.
In terms of your italicized post, I don't see why the fact that someone is the product of their environment vs. a product of biology etc. matters, because those factors are outside of the control of the individual regardless. We should judge people on their actions and choices. Whether or not someone grew up in the 1950s South, if they made an intentional choice to join the KKK and intimidate civil rights activitist, whether or not they were "evil" from birth is irrelevant.
People, IMO, confuse the fact that someone can be understandable (e.g. Dexter is a serial killer because he saw his mother chopped up in front of him) does not mean it's justifiable.