I'm afraid that I can't answer the question of when people began to worry about punishing rape -- thats a question which would probably be best answered by someone who specialises in prehistory. My answer will be focused on medieval England, but the processes are themselves pan European. To a certain extent, the issue of consent in medieval marriages was irrelevant. The act of marriage was a pledge of perpetual consent to sex -- a man could not rape his wife and vice versa. Both parties had the perfect right to demand the 'marital debt' (sex) from each other. Failure to provide this was one of the few grounds upon which the church would grant an annulment. As for rape outside marriage there are some examples that we can draw on, once we begin to get detailed court records. However, these cases tend to be very few and far between. In medieval England, as today, it seems likely that shame and a paucity of evidence made it very difficult to bring a successful prosecution to the courts. A further impediment was that the idea, which still survives today when people like Todd Akin spoke of 'legitimate rape' while running for the US Senate, is that if a woman fell pregnant as a result of a rape, it was presumed that she must have enjoyed it and that therefore there was no rape. It is also important to note that these cases were almost never brought by women themselves. Women in medieval England, unless they were unmarried widows, had no legal standing and their husbands or fathers had to sue in their place. Therefore rather than the consent or not of the woman in question, the cases were framed around the economic damage sustained by the man -- for instance a defiled daughter might be worth less as a marriage partner.

To the medieval mind the only point at which consent was ever relevant was the decision to marry at all. So for the first thousand years or so of the Christian era the idea of consent to marriage was not something that people seem to have been concerned with. Families brokered marriages between themselves and the participants had no legal standing to challenge the authority of their parents. The transformation from a system where marriage was arranged within families to one with a greater input from the people involved can be attached to the growth of the movement for church reform in the 11th century. As the central Catholic church began to increase its power and develop the mechanisms of canon law they began to regulate the practice of marriage. From a theoretical point of view this can be seen in the writings of men like Peter Lombard, who argued that marriage had to be consensual and need not be consummated to be valid, and the great canon lawyer Gratian that marriage could be created by sex and a promise to marry later or the marriage and then sex. The minutiae is not particularly important, but it is worth stressing that marriage and therefore permissible sex could only be consensual. This is also important because it put considerable power into the hands of the couple. The church's new teaching made the equivalent of a modern Vegas wedding a possibility no matter who the parents would have preferred people to marry. TO sum up "marriage is contracted by consent alone" (William of Pagula) Quite quickly, even before the above were formalising this we begin to see its effects. Christina of Markyate, (c1100-1158) provides a good example of this in Anglo-Norman England. Despite the persistent attempts of her parents, who even invited her prospective husband to rape her, Christina asserted her right to consent and ran away to become a nun/mystic. Now, it could easily be argued that her case was an exceptional one and that most women and girls would have been pressured into marriage by their parents, but it is important that the option of refusing was there. In practice it seems in noble families parents often went to great lengths to try and arrange a marriage that their children would be happy in, often in close consultation with them. Lower down the economic spectrum women likely had an easier time picking for themselves because their marriages implied a smaller transfer of property -- although there is a lot of detail about seigneurial control over peasant marriages which i could put in a separate answer if people want to read it.