You have been handling an extremely painful and taxing and emotionally exhausting "sector" of all this bullshit that married survivors go through - and doing a great job of it from what I see. Open-eyed, honest, identifying problems and what's really important. And it's clear that your wife supports you and the help she is getting will be critical for both of you.
When I met my wife, 7 years ago, I barely knew about my CSA - they were meaningless dissociated pictures in my head devoid of any feeling - and I didn't care about it at all. So she knew and saw nothing at all. The time bomb in my head finally blew up a few months ago - between the shame and horror and shock of it, plus other life stresses we were going through, I couldn't tell her. I kept up my lie about another month, then she found my pills and I had to tell her. And we each had to deal with our own shocked and changed spouse for a while.
I know what it's like to hurt her with lies, to feel like the piece of shit who hurts his wife, know what it's like to wonder if this is the final step, the beginning of the end. She, too, is very suspicious and creeped out by MS - it doesn't help that she used to snoop here and learned that way that I'm bi (or have SSA, whatever). But.... she dealt. She dealt, overall, quite well. She's still on edge about secrecy issues, but in nearly all regards she's firmly in my corner now.
If anything she's become more affectionate since learning about the sexuality issue, maybe she wants to make sure I don't forget where I really belong. Makes for a nice "consolation prize" I suppose?
Oh, and... CSA or no CSA, I think nearly all marriages have the "wish-I-hadn't" moment. No you shouldn't say it, but we can all be adult enough to admit it can exist. It's difficult to keep going under the BEST of circumstances, so every extra stressor can only naturally make the dark thoughts swirl a bit more. They're only thoughts. Marriage, in general, can be protected a bit better by the "they're only thoughts" factor.
You really seem to be on the right track and I'm rooting for you and your wife to come through this closer than before.
"Don't think it hasn't been a little slice of Heaven just because it hasn't!" --Bugs Bunny