His wife claims that she was raped

Praise be to Allah.

If what your wife has recently told you is what really happened, then she has committed a major sin and an act of clear betrayal by giving in to this attacker and not trying to escape or stop him or call for help and so on.  Her claim that she was forced to do it is not acceptable, because she makes no mention of being threatened with a weapon or being tied up, etc.  If this is indeed the case, and she clearly did not try to defend herself, then what should you do and how should you regard her? 

There is no doubt that you should warn her and remind her about Allaah and the Last Day and its horrors, and explain to her the seriousness of overstepping the limits set by Allaah and betraying one’s spouse. You should also remind her of the terrible punishment dictated by sharee’ah for the married person who commits adultery, which is stoning to death. 

After warning her in this fashion, if you see that she regrets what she did and is striving to be righteous, there is nothing wrong with staying with her, and your marriage will still be valid.  It seems most likely that this woman is indeed sorry for what she did and has repented, because she is the one who has brought up the subject after it had been forgotten, and she has told you about it. Perhaps this is because of her guilty conscience and sincere desire to seek forgiveness from her husband.  The sin that she committed when she was very young and living in the ignorant environment of America, and where she may have resisted at the beginning of the attack, then softened, is nothing like the sin of a woman who goes out of her way to commit it, and plans to do it deliberately. Our advice is that if this woman is now righteous and truly regrets what she did, then you should forgive her, especially as you may by now have children who will suffer if you divorce her.  At the same time, you should continue to teach her, keep an eye on her and not stay away from her for too long.  We ask Allaah to acceptance repentance from us all.

 Finally, I want to address a serious matter that you refer to in the second part of your question, which is the fact that you say you no longer want to go to the mosque or pray or make du’aa’, because of the crisis that you are facing.  This is very strange, for whenever the Prophet (peace and blessings of Allaah be upon him) was faced with a serious matter he would turn to prayer and ask Allaah to help him, and he taught us to do likewise. We should not turn away from the houses of Allaah (mosques) or stop praying and making du’aa’. Where else can you turn in times of trouble and who else can you ask for protection in this crisis? Turn back to Allaah, my brother, ask Him to relieve your distress and seek His help with patience and prayer, for Allaah is with those who are patient.