As for me, I think that the abscence of a father is a hint that Sonomi really loved Nadeshiko in a romantical way and that she could never find anyone else to love, because Tomoyo doesn't act like she has had a childhood troubled by an abusing parent. I see no reason as to why CLAMP wouldn't throw in a quick scene of Tomoyo's dad somewhere, or mentioning that her parents were divorced, if it weren't for them wanting to hint at something.
What do you people think?
Hmm...
Perhaps, she just wanted to find her own happiness to get over her loss to Fujitaka for 'stealing away Nadeshiko.' It reminds me of Mayuko-sensei in Fruits Basket Volume 10 where she dated Shigure but out of loneliness. I believe that after a while, Sonomi just couldn't really be happy with her marriage to Tomoyo's father (who I decided to call Daijouji.) She ended up divorcing Daijouji and raised Tomoyo on her own.
Moezy-chan: I admit to not knowing that much about the modern Japanese society, so - how common are arranged marriages nowadays?
...I just thought Tomoyo's father died a very, very long time ago...
I've watched only the locally dubbed version of the anime and, in our place, dubbers want to make shows children-friendly... ^^;
Come to think of it, Tomoyo-chan never mentions her dad. I think he's passed away... I guess it's just... complicated.