It is not made known to the player.. but, if it was something important, such as Ross killing Abigail, I'm sure it would have been shown and Jack would have said something to Ross about her.
So most likely natural causes.
It could have been pneumonia, or tuberculosis. While Marston is in the ranch in the evening, Abigail wil occasionally cough.
thats all wrong abigal die three year after johns death. the causes were unknown