I didn't get any good responses when I asked about this earlier this week, so I did some research.

John Unruh's The Plains Across is older but still considered top-notch scholarship on the Oregon Trail and its counterparts. He discusses previous estimates of mortality that range from 6-10%, criticizing them for relying too heavily on modern stereotypes of "Indian attacks" (a very tiny factor), extrapolating from particularly bad epidemic years of cholera to the period overall, and relying too heavily on the emotional accounts of travelers describing deaths in the midst of their wagon trains. He suggests another estimate, 3%, is probably a little too conservative in under utilizing diaries.

"My own reading of emigrant counts of fresh graves, statistics reported by trailside observers, and estimates by overlanders themselves" gives Unruh an estimated 4% overall mortality rate.

Disease was the big, big killer, especially cholera. As far as particular causes of death for different groups, one thing that comes up in women's diaries of the trip especially is children crushed to death by wagon wheels.