Hi Gman,
I am glad you did not rush into a divorce. Firstly, I will say that no behaviour justifies her adultary - you may not have helped the situation, making it possible for you to have empathy with her temptation but it is still her that is accountable for her actions, as you are yours. If she has accepted this responsibility, then forgiveness is key if you are to rebuild any trust in your relationship.
On the matters of rape and pre-marital sex. Again, like Raymond, I will assume that this was before she was saved and instilled with the Spirit of God within her.
Speaking from a female point of view that is a convert to Christianity and has been raped and sexually molested as a child and having lived with and encountered may women from similar backgrounds - sometimes these experiences can remove the value of sex or truly intimate experiences. Not all women feel this but many do and it leads to adolescent insecurities and can actually make them more prone to having one-night stands or whirl wind 'romances' because sex is sex - it has no value, the value it had has been stolen from them. This can take councelling to address this and for the woman to make her peace with it.
Moreover, if you came to Faith before having your first sexual experience - that is what God intended for you - that is just your Spiritual Time Line so to speak. We all have one, hers' was just quite different from yours. Granted, however, she should have been honest with you about her past - of that I have no doubt. It is quite possible that she felt ashamed and that you would think she would be an unworthy wife if she were to bare all (not that this fear or attitude makes the deceit right by any means but more understandable, but not justifiable).
And given the fact you had only been in a relationship for 6 months before marrying - well, maybe she just wasn't comfortable enough with you yet to share such intimacies. I do have to commend her for having the courage to tell you about the rape, it is no easy thing to talk about. When you talk about it - you relive it almost. No matter how much you try to block it out or objectify it, it still happened, it was vivid; unwanted and leaves the victim feeling tainted. Just like Tamar did went she put ash on her head and tore her virgin gown - this is the physical representation of how a woman feels when she is raped: Tainted/Unclean
I truly hope that you could fully forgive her for her lack of openness at the beginning of your relationship and marriage as she will be as aware of your anger and sadness as you are and it will drag you down together as you are one flesh, you act as one.
I would suggest true sorrowful prayer, ask God for His strength to Forgive. It is no easy task! Holy Forgiveness outweighs any human forgiveness we can muster. We must be Charitable, Faithful, Gracious and Hopeful in God's definition, not our own half hearted versions, full of ifs and buts. Only He can heal your woes, and after this, as her husband hopefully you can tend her wounds too. And you can grow with each other in light of God and Glorify Him in your marriage by the way you react to and respect each other.
Remember, Love is Patient, Love is Kind... Love holds no record of wrongs. The Father doesn't and you are in His image - this is your aspiration as a man of God, hold her and I pray you can really forgive her for all her transgretions and pray she forgives yours as none of us are perfect.
Love and Peace be upon you my Brother!