My heart goes out to you and your husband. He has been through a big trauma and this is going to take some time. It seems like he is pushing you away as a way of dealing with things. Intimacy makes us feel our existential pain and when he gets close to you, he feels his feelings more. He is angry at himself (even though things weren't his fault, his feelings are irrational), he's filled with shame. His counsellor will help him with this (you should see a counsellor, too).
My advice is that you don't coddle him. I know you want to be there for him and show him love, but the best way to go about things is like any other marriage. He doesn't want your pity or for you to tip-toe around his sexual issue, he wants to be there FOR YOU as a man, he is just overwhelmed emotionally.
As his woman, I suggest that you open your heart and tell him this: "I feel lonely and I don't want to feel this way. I want to be affectionate with my husband and I don't want to feel shut out. What should we do?" DON'T say anything about the trauma. Don't say, "I know you have been through so much." or anything like that. Just state your feelings and wants and never address the trauma.
Don't feel bad about having these needs and expressing them (he doesn't want your guilt, pity, anything like that), but be sure to do so from a loving, soft, vulnerable, feminine place inside you. Be direct, be honest, be firm about what you want. Treat the conversation like you would if he hadn't been through the rape and was just disinterested in sex. Make sure you let your vulnerability "bleed out". Write him a letter if you want. Make all your words about how you feel and what you want and don't want. If he gets upset or feels pressured, just say that you are only expressing yourself to feel closer to him through honesty. Listen to him and feel free to leave the room if he gets to irate. No coddling, remember. No letting him get away with bad behavior. He doesn't want you to let him.
If you do sleep together, don't ask him how he feels or make it weird. He desperately just wants to feel like a normal man again. He will get there.
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The best way for the two of you to get back to having sexual intimacy is to start slowly. When I work with couples on their sex lives we go through a program, where there is no pressure on intercourse. The two of you do home assignments where you slowly connect with each other then we all talk openly about the experience. It works very well with any type of sexual problem even rape, erection, orgasm issues. One of the main issues for men is that they are expected to be the person who knows what to do, in control, and this can create performance anxiety.
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