And now i also have to remind myself that it's his brother who runs the show so who knows how he wants to handle things.
Actually it's his brother, his sister-in-law, and his
Angel collaborator Jeffrey Bell. I feel so sorry for Bell, since everyone keeps ignoring his presence on the show, even though he has far more TV experience than the Whedon-Tancharoen duo.
In the comics at least, racial purity and eugenics was part of their original goal. They were after all the science division for the Third Reich. Marvel writers basically turned them into a generic bad guy organization as early as "Nick Fury, Agent of SHIELD.
Just my point -- their goals evolved. And as I said,
The First Avenger made a point of showing the Red Skull breaking HYDRA away from Hitler's ambitions in favor of his own goals. Even then, it was clear that their loyalty was to the Skull and to better conquest through science than it was to Hitler, his party, or his ideologies.
And in fact, lots of rational people join organizations with harmful or misguided or evil goals.
You are confusing "normal" with "rational". I don't think a rational person would join an organization that has evil goals, evil methods maybe but not goals. Could the average person join an evil organization, sadly yes but if you look at these people, they too have "issues".
I'm not confusing normal with rational; I'm saying that "rational" is not a value judgment. Many people use what they believe to be rational arguments to convince themselves it's justified to do evil things. Again, nobody really considers their own actions and choices to be "evil." People who join HYDRA would do so because they believe that greater power will help them achieve their goals, or that freedom and democracy don't work and people need to be dominated and controlled for their own good, or that pure science matters more than morality so it's okay to pursue any kind of research even if it kills millions of people. They're not doing it because they want to be villains in a story. In their own minds, they're pursuing a positive goal.
Pierce was a classic psychopath. All of HYDRA agents are pretty much psychopaths.
Maybe, but psychopaths are often extremely rational. They lack empathy and remorse, so their choices are often based on cold calculation. Again, calling someone "rational" does not equate to calling them good or just.