Both you and your husband have been through a great deal of trauma. Remember how he was before he saw his councilor? Closed off, un-talking, cold, distant? And it took seeing a councilor to whom he could spill his guts to, to start letting you see the man you remembered and to confess to his adultery to you. (And I hope that he is continuing to see that councilor.)
I do not mean to make light of his rape. I've been there more than one time. It's a horrific thing to have happen, I would guess, possibly even more horrific for a man who has not considered that this might possibly happen to him, unlike women for whom, IMO, the possibility of rape is always in the back of our minds.
My FWHs ONS and his cyber-sexcapades were a far worse trauma to me, than my rapes. My rapes haunted me. My FWHs betrayal shattered me. I'm still picking up the pieces and trying to glue them back together.
So please. Know that you have gone through some horrific trauma yourself. At one moment, you were happily married. In another moment, you were facing a stranger. And the next moment, you found that you were betrayed by your husband who vowed before God to have no one else but you.
That's trauma. Just as he needs to let what happened to him out so that he can purge it, get the support of you, his church, his pastor, you need to do the same. YOU need to talk about this until you don't need to talk about this anymore. Please do consider seeing a councilor. If you don't deal with your trauma, I guarantee that it will come out in other ways, in another time. You cannot ignore this, nor sweep it under a run. It will simply grow and become a monster.
You need to keep talking. He needs to keep digging why he decided to betray you, and make no mistake, it was a decision, not a mistake. If you two are to heal and to heal together, you need to be utterly honest with each other and seek support. IC or MC or a combination of both.
I'm not going to lie to you. It's hard. It's the hardest thing that I have even done in my life. God and I have had some interesting conversations, some of which have been with my fists clenched and screaming upwards at heaven. It's not been pretty. But if the two of you have the earnest desire to R, you can. If the two of you can be utterly honest with each other, seek understanding, and ultimately have compassion for each other, you can make it. It sounds to me like you had a good marriage before, with work, you can create a good marriage from this point on. I would like to suggest that you read both "Not JUST FRIENDS" by Shirley Glass, and "Beyond Ordinary" by Justin & Trisha Davis who are the founders of RefineUs Ministries. I found both to be quite helpful.
And keep coming back for support. Christian, Agnostic, Muslim, Zocasternarian, we are all human beings who seek the same things. Love, support, comfort, and community. We are all here for you. (((hugs)))