Having read the book, I understand the following. Matt, who had presumably died of his illness in the original timeline, remained dead without children. Bran, who had married Zillie in the original timeline, now married Zillah. Gwen, who had married Gedder in the original timeline, now married Rich (whom Gedder had originally murdered). My question: where did Chuck and Beezie, and their father come from? All the Maddoxes and Llawcaes in the 1865 arc were either dead without descendants, or married completely different people, altering their bloodlines forever.
There seems to be some heavy In Spite of a Nail going on with respect to specific people, in that even if you change who someone's great-great-great-grandparents are, they still end up being basically the same person (unless they're not, like Madog Branzillo, although it's hard to tell what the extent of the change there was. He could be an entirely different person who coincidentally has the same name and office, or he could be the same person with a different temperament). There might also be some form of You Already Changed The Past although obviously that can't be applied to every part of the plot.
It seems to be more that Gaudior wants Harcels and his people to do a culture-wide Dying as Yourself rather than see them be corrupted into learning the ways of violence and war.
So Gaudior has decided it is better for these people and their entire culture to be completely destroyed, precluding the possibility of them helping others or stopping other genocidal groups in the future, than for them to realize that they could use force to protect themselves. The 'good' option is for these people to be killed off. That's a heck of a case to make in a world where genocide has been stopped by force and the world seems to be a bit better for it.
To be clear, we're not talking about a tribe learning to defend itself (or not), we're talking about a child witnessing (or not witnessing) a violent act, and possibly being traumatized or corrupted by it. It is implied later in the story (and in An Acceptable Time) that the People of the Wind are capable of defending themselves.
Then what was the point of Gaudior's comment that they were 'a people of peace' and that 'your planet does not deal well with people of peace' when Charles Wallace asked what happened to them? Was the unicorn just being an asshole who wanted to suggest that they had been wiped out?
Gaudior is kind of a jerk. I wouldn't put it past him.
So by making sure that certain people win or survive Charles Wallace is helping alter a man from a military dictator into a peace activist. Is this book encouraging eugenics?
Seems to be more of a Set Right What Once Went Wrong, as Gaudior implies that the book actually starts in a timeline caused by a Might Have Been that the Echthros almost made come true.
Except that everything that sets things right involves making sure that the right person went on to have children. One of the pseudo-psychic characters even states at one point that it's 'wrong' for the people of one bloodline to mix with the people of another bloodline. We are effectively being told that if only a certain men had married the love interest instead of the other bad person hundreds or thousands of years ago the world would have avoided nuclear war in the late 20th century.
Having children is more than passing on blood or DNA. It's also passing on ideals, beliefs, and other intangibles. By changing the ancestry of a genocidal madman, Charles Wallace ensures that, in the corrected timeline, Branzillo is raised to respect life rather than to seek destruction. The warmongering Branzillo, raised by his violent ancestry, sought to impose his will militarily. However, when he is changed to the more moral and peaceful "El Zarco," raised by his more peace-loving ancestry, in the end he seeks to instead prevent a war that would cost millions of lives.
So we're to assume that every single person of that line was a horrible, unlikable, violent person who raised their children to be precisely the same? And that every single person of the other bloodline was raised to be a perfect person who loved nature and would never do something awful? That sounds an awful lot like saying that ancestry is all that matters and if you're born of the wrong bloodline you will be a horrible person no matter what your personal opinions or circumstances may be.
But Gedder and Zillie were adopted by a perfectly normal farmer. They have very little connection with their biological parents, and Gedder still turns out to be a power-hungry bastard, who mustn't be allowed to marry Gwen, and Zillie... is still a pretty girl who mustn't be allowed to marry Richard.