The execution of John D. Lee was actually quite accurate. He was the only participant in the massacre that was ever tried, and after two trials, he was convicted. The army took him out to the massacre site on March 23, 1877 (nearly twenty years after the event occurred), and then ordered a firing squad to execute him. His body was buried several miles away from the massacre site.
The remains of the victims were buried in the days following the massacre. However, the graves were so shallow, that within a few days, many of the bodies were dug up by animals. Two years after the massacre, remains were gathered up from the area by a U.S. Army Corps and buried. A monument was built over the grave, with a cross. "Vengence is mine, I will repay, saith the Lord" was inscribed on the cross.
There is a memorial dedicated to those who died in the massacre. It is in Washington County, Utah.
Nancy Dunlap (the "woman in pants who carries a gun") died in the massacre, not before. So did her husband, Lorenzo, who is said to have died before the movie's action takes place.
John D. Lee had nineteen wives and sixty-seven children. At least eleven of his wives eventually left him.