Mostly the Bible is misread especially by those who choose to fight against Christianity. Take an example mentioned in OP the woman rape in OT. The Jews as a whole were slaves of the Egyptians. Their women can be "legally" raped by the Egyptians. Moreover, a Jew raper cannot be punished hard for the reason that he's a property of his Egyptian master.
So the most efficient way to protect women is to hide them deep inside the house. So what mentioned in OT mostly dealt with women who actively went out of the house (her hiding place) to try to attract men. There were virtually not many actual raping occurred, as by the very culture of the Jews that they seldom hurt their own people this way. In the case when it did occur, the 2 families would have to settle it either with compensation, or with life time commitment by marrying the woman. Punishing the raper may be out of option. The raper is the asset of his Egyptian master.
By disregarding this historical factor, a lot will read the Bible as if it encourages raping.
The laws handed down through Moses came after the exodus, so none of that would apply.
Such a culture was formed long before Moses. Moses followed what was efficient at that time. The Law was set before they entered Canaan.