The passages in which rape was condoned is usually greatly misunderstood.
For example: Some people state God once allowed soldiers to take foreign virgin women. The passage is none as horrible as it seems. The women were not raped. In reality, they would often save women and children during war (instead of slaughtering them). They introduced the women and children into the community through marriage. Since marriage, back than, was often arranged (marriage was rarely out of true love back than) it wasn't as bad as you would think. Not to mention the women often were given special laws to protect them from evil husbands.
Another passage is believed, by atheists, to allow sexual slavery. In reality, it does not. Poor families would often give their daughters (and sons) away to work as maidservants to the wealthy. It became the 'masters' responsibility to act as a father to these young women and as a father figure they would protect them, and even arrange marriages. Many times it was to his son (so the poor girl marries a wealthy man). These young married women were given great laws to protect them. If her arranged husband ever abused her, neglected her (or her children), or refused her medical attention, food/water, clothing, or married a second wife she was allowed to divorce him.
Rape, in the bible, is serious offense. The rapists were given the death penalty. Although virgin women were also give the option to marry their rapist if they chose (since it would be hard to find a husband as a non-virgin). Despite popular belief, it was never forced. Both the daughter and her fatehr had to consent.