She knew her husband was raping their children but didn't care, if we can believe Harriet. Harriet says,
"My father could have raped me in the middle of the living room and she wouldn't have noticed. She was incapable of acknowledging that anything was wrong in her life or mine."
Isabella is also aware when Martin begins to rape Harriet, and does nothing to stop it. When Harriet returns, Isabella claims Harriet's an imposter, and dies soon after.