It is said that Talmud passages declare a man’s right of seducing and marrying 3-yr old baby girls. Simeon ben Yohai upheld the privilege.
Kethuboth 11b When a grown up man has intercourse with a little girl it is nothing….the intercourse of a small boy is not regarded as a sexual act
What is the current rabbinical answer to the pain, physical, and psychological damage caused by sodomy, which is necessary for raping a boy, and for the extreme pain, physical and psychological damage done to little girls?
The torah does not allow or permit anyone to cause extreme pain or psychological damage to another person. The reason you have are having a hard time understanding what was transpiring then, is because you are superimposing your societal values, and your worldview on the society, culture and psychology of people that lived in a totally different society, who had very different life conditions, and had totally different values, and a very different view of what marriage was about. In their society this was not a man that was sodomizing her, but her man that she was married to. As far as the actual relationship between the two, to this girl, this was the man that she looked up to, and the man that gave her all of her needs, housed and protected her in every way. She was very happy with this arrangement. Let us take an example of Rivka, who was age three when she told her mother and brother that she wants to go get married to Yitzchok whether they like it or not! This is exactly what she wanted, and any union that there was between them was out of love and devotion to each other, and not quite with the negative backdrop that you are describing. (Yes it does come because they looked at marriage very differently than we do.)
It is true that in our society we look down upon a marriage where the father decides to marry off his daughter without her consent or permission, however in their society this was the norm, and it was the accepted way of life, and no one looked down upon it.
As a side point, when the gemora discusses these topics, such as the halachic ramifications of a biah of a katan or to a ketana it was discussing it from a scholastic angle, according to Jewish law, how is this act categorized. This would be no different than any other law book that is discussing the legal ramifications of an act and not the psychological ramifications of the act. For that there are other gemoras that discuss the issues of the damages that can be uncured.
I hope this sheds some clarity on this issue.