By skyforbes The argument would be fear. I'm assuming she was scared of Michael and his aggressive personality. Whenever Kay tried to talk to Michael, he screamed and berated at her, so she chose to accept her new reality.
By the 2nd half of Godfather Part II, Kay had enough. She survived a shooting, her family nearly slaughtered and Michael had some kind of involvement and this time, she won't allow Michael to intimidate her into silence. Admitting the abortion was the only way Kay had to make sure Michael would let her go because she knew Michael couldn't stay married to a woman who killed his son.
The question I have is: what prevented Michael from putting a hit on Kay? She killed his unborn son, she knew too much, she abandoned the family.
I think he might have been tempted to kill her but she bore his children, he could never kill the mother of his kids and I also believe, deep down, he still loved her. Not as much as Appolonia but she was the other woman in his life.