It was in 1972 that Joanie left her husband Clinton and her children. The point where Joanie knew that her marriage was over was when Clinton had some bowling buddies over, and when one of them complimented her on her cooking, her husband said, "My wife--I think I'll keep her." And then she broke his nose.
Joanie, husband and kids were living in Denver when Joanie ran out the door and into Mike and Mark on their motorcycle, touring the USA on their school break. (Mike was in the sidecar.) http://www.gocomics.com/doonesbury/1972/09/10
Clinton came out to Walden to try to get his wife to return, using a tape recording of their youngest child, begging for her mother's return. Zonker headed him off, and as Clinton refused to give into his wife's demands (something about saluting the Sisterhood), he left.
Joanie lived at the commune, and got work at a daycare, and that's what's going on, if you go to the Doonesbury flashback, you can read that 40 years ago, Joanie was teaching in a day care. http://doonesbury.slate.com/strip/archive/flashback
I'm not sure when the custody trial occurred, and I have no idea whatever happened to Clinton. I've sent a letter to Doonesbury, asking about him, and will post here if/when I get an answer.