28 If a man find a damsel that is a virgin
, which is not betrothed, and lay hold on her, and lie with her, and they be found;
29 Then the man that lay with her shall give unto the damsel's father
fifty shekels of silver, and she shall be his wife; because he hath humbled her, he may not put her away all his days.
Things to focus on in bold. As mentioned earlier, these matters are not instances of a rapist, a victim, and a judge but all of the above plus (rather especially) the families of the rapist and the victim. Religion is a reflection of society, and for societies where the tribe is still powerful concepts like this persist. It does not occur in religious societies that have discarded the tribal unit for the immediate nuclear family or individual.
In the above, we have the situation where the head of the family, the patriarch, is the one who is deemed the wronged party.