There are probably many ways to look at these verses.
First, there are so many conditions here (“if she is a virgin”, “if they are discovered”, etc.)
Second, what’s a shekel, especially in those days? What is 50 shekels? – the price of a slave, or something?
Third, unattached women had very low status, so forcing her to marry is a form of “social security” for her. It’s also some social security for the child who might probably be assumed to result from the intercourse and this is no small matter.
Fourth, this precept of the law is surely intended to be a deterrent to what it describes.
Fifth, to an atheist, in modern times, it may seem that what is described here is just a normal variant of behavior. After all, with an atheist, we’re dealing with someone who inconsistently might assert absolutely that there are no absolutes (duh). So, the atheist is saying this ex-virgin should not have to get married to this sex offender and maybe other more modern and purely pragmatic actions should take place, like legal prosecution, morning-after contraception, abortion, etc.
Although it is popularly contested, Judeo-Christian beliefs point to the equal dignity of men and women. Again, one has to seriously consider the deterrent purpose of this law and that the Torah, in fact, metes out a certain measure of divine justice (and mercy) here, for example, that the sex offender is not put to death for his action. Rather, there is, as we might say, a fine and an automatic life sentence imposed – unsavory as the whole mess might be.
Atheist or otherwise, we should not jump to hasty (or any) judgments of God’s laws.