They had been married for five years when, in 1853 Becky gave birth to a stillborn son. Soon after that, pain and soreness persisted in one of her legs. Morgan took her to doctors all over the country, from New Orleans to Hot Springs, Arkansas in search of a cure, but to no avail. She apparently had septic thrombophlebitis, an infection of a blood clot in a leg vein, which caused the arteries supplying blood to that leg to shut down. In those days, the malady was called "white leg" or "milk leg" and there was no known cure.

Becky's condition grew worse, and in January of 1861, her leg had to be amputated. After years of suffering, she died on July 21, 1861, the same day as the first battle of Bull Run.