A friend of mine has been raped. She is very disturbed about it. In what way can she atone for this so that her sense of guilt is lessened in front of God?

There are two possibilities why the unfortunate incident happened to your friend. It is possible that she did nothing to blame at all, and somebody just did it to satisfy his animal desire. It is also possible that your friend allowed the person the kind of liberty that ultimately inclined him to go to the extent of raping her.

In the first case, your friend need not worry about it. Indeed it is understandable that she has been emotionally bruised. However, she should take solace from the fact that the Almighty is extremely forgiving and sympathetic towards those people who have been a target of callous behaviour of others. The Qur’an tells us that there were people at the time of the revelation of the Qur’an who used to force their slave girls into prostitution although those ladies were not doing it willingly. The Almighty says about them:

And if anyone forces them into it, then surely after such a compulsion, Allah will be forgiving and merciful to them. (24:33)

If that is the case, your friend should not feel guilty. Allah is definitely merciful to people like her.

However, if your friend did allow the man some liberty to come close to her, and then on finding her unwilling to have sex with him, he forcibly fulfilled his desire, then she too has to be blamed for it. In that case she should most certainly seek forgiveness from the Almighty as much as is possible, and, in addition, should firmly resolve to adopt an attitude where by men do not come as close to her as to cause that possibility to get repeated.

Allah Almighty has desired that we be careful about the members of the opposite sex to enable us from avoiding the possibility of the kind of embarrassment your friend has gone through.

(http://www.islamicissues.info/qa_question.php?qid=273)