That's pretty damn good I think. Oftentimes there's no pretty outcome possible...you just have to run damage control and work your arse off until the storm clears.
Just let her parents and the community do some work for you now. She will come around I think.
If she does ever say "I don't want to be married to you" you can always say "I wouldlnt' want to be married to the guy I was when you left either...I dont' care for him at all...I am in a much better place now, which is much better for all of us."
"I am not asking you to be married to that guy...I wouldnt want to either" I am sorry about my part in how difficult things got. That was not a mature way to handle problems in our marriage and I wasn't thinking of our family at all."
"I am now and I am not going back there. Our life together from this point on I have no idea how that looks or where it's going yet...that's up to us to work out. As long as we have our son we are going to be connected, I just want that to be the healthiest connection for all of us. I think our son would be very upset if he fully understood what was happening. He will one day and I will have to do my best to help him understand we forgot how to be good parents and friends for a while, but we learned again."
That may be too much, its just a draft...some material for you to pick and choose from.
The point is make her realise there IS a door open making her feel any pressure to enter or not. I think she may have felt there wasn't a door there in your convo...your call there. Always help her feel the door is there.
When she blurts out statements like "we never agree on anything" as calmly as you can find a way to help her feel like there is hope and common ground :
"We agree our son should have a good home, and we agree we should be as kind as possible to each other. I am doing my best to be everything I can for this family. I am really upset sometimes about how this is going to hurt our son. I really am just trying to take the time to fully assess the impact of permanent sweeping choices on this family. We aren't just two people, we are a family."
"Our son is common ground, he always will be. I am not going to do anything to hurt him or you, and I hope you can find the means to feel the same."
I dunno...just try to make her feel like the conflict between you two is in HER head and there is hope. She's saying negative things because she's miserable...it happens...when people feel sad and hopeless, they get REALLY NEGATIVE and pick a punching bag. You just have to take up the cross and carry it for her until she gets centered again.