How are women treated throughout the book?

In short, poorly. The women in this book are routinely mistreated and abused. Esi is beaten up by Big Man and various other characters and is eventually sold into slavery where she is whipped and abused by her master routinely. Abena is blamed for poor harvest in the village, and she is eventually abandoned during her pregnancy by her fiance. Effia, the sister of Esi, is sold into slavery as a child.
There are numerous accounts of abuse of women in this story. The point of all of this mistreatment is to show the true picture of how women were treated, historically and in societies like this one. While there were great things and wonderful tales that could and should be shared about these societies, it is imperative not to gloss over the suffering that many endured at the hands so so-called "great men".

Homegoing features a wide variety of female characters. Both in West Africa and North America, their social statuses range from low to high. During much of the period covered, both areas allow slavery, so women may be enslaved or slave owners. For example, Esi’s father was a great Asante warrior who bought a girl slave for her. During an attack, however, Esi was captured and then enslaved and raped. Her life changed from one of ease to one of dire hardship. Her half sister Effia, in contrast, was a child slave. As an adult, she married a British slave trader. Another Asante woman, Akusoa, was resolute in refusing to marry the younger James as long as he was a slaver; she changed his life. However, he was deemed unlucky, and this was extended to his daughter, who was blamed for bad harvests. In America, Esi’s duagher Ness was a plantation field worker. She was whipped and, when she and Sam tried to escape, he was beheaded, and she was sold away. Within several generations, her descendant becomes a famous jazz singer. In sum, female characters appear in many different situations and often survive devastating hardships.

In the book, women are physically assaulted for no reason; Big Man beats up Esi in order to maintain his macho image and not be mistaken for a weakling. After Esi is enslaved, she and the other women are inhumanely chained, stacked together, and locked up in the dungeons. In addition to that, they are raped by the soldiers and deprived off their dignity. Esi continues to endure physical torment once in the hands of her owner, who whips her every time her child speaks a word in her native language. In fact, her child is a result of rape.
Women suffer victimization and are treated as commodities. When Ohene fails to get a good harvest, the entire village blames Abena for ill luck. Ohene promises to marry her only when the harvest improves but eventually betrays and abandons the pregnant Abena for another woman’s hand in marriage.
Even though men experience slavery and segregation, women bear the brunt of the suffering because they struggle under the institutions of patriarchy and slavery.