Let me be clear here: this is a hypothetical case. It did not actually happen, nor has it ever happened. In fact, it is so obviously implausible that no-one would dare use this situation as an excuse, and if they did, the only possible conclusion is that they were lying. The Talmud does not condone this as an excuse.
So then, why do the scholars include this hypothetical if it’s useless for actual rape cases? It is to illustrate a particular legal point: namely, that in Jewish law, intention matters, but monetary compensation is just as important. They do this by considering this highly contrived case, which would never happen in practice but makes the point as clear as possible. Of course, it is nearly impossible to rape someone accidentally (though see below). But the principle sets a general precedent for other cases, in which a lesser crime might have been committed unintentionally.
(Curiously enough, a few years ago there was a high-profile case of ‘accidental rape’ in Australia. The man claimed he thought the woman had given him consent; the woman claimed she had never given consent. I can’t seem to find a link, but if I recall correctly, the judgement was eventually in favour of the man. Modern laws have edge cases too! And applying Rabba’s dictum here would actually have given a fairer result: the man would still have had to compensate the woman for any injuries.)
> You don't have to renounce your faith to admit the text is flawed, human. That's all I ask that people learn.
Of course! Texts are human, and the Talmud especially so: it’s literally a record of a bunch of people debating with each other and criticising each others’ legal interpretations. But this particular part of it is not problematic.