Lisa McPherson, 36, died Dec. 5, 1995, after being under 24-hour care at the church's Fort Harrison Hotel. An autopsy showed she died of a blood vessel blockage in her left lung that was caused by "bed rest" and dehydration.
CBS News Legal Consultant Kristin Jeannette-Meyers reports that church records show that after 17 days in isolation, McPherson was driven by church members to a hospital - not the closest one, but one 45 miles away where a church member was on duty. She died on the way.
The church was charged with abuse or neglect of a disabled adult and unauthorized practice of medicine, both felonies. It faces a fine if convicted.
No trial date was set. In its court filing Monday, the church requested a jury trial.
McPherson's family has filed a wrongful death lawsuit seeking unspecified damages against the Los Angeles-based church, saying she was held against her will after trying to leave the church founded in 1954 by the late science fiction writer L. Ron Hubbard.
Church officials say McPherson was well cared for but became violent and incoherent, had trouble sleeping and resisted efforts to give her food, liquids, and medications.
Dennis Erlich, who was a Scientologist for 15 years, says the treatment McPherson received was standard for church members with psychological problems.
"The step consists of locking a person in a room where they cannot communicate with anyone, and they're to be kept there until they supposedly come out of their psychotic state," Erlich said.
The church refused to comment on the charges. But, a year ago, Scientology's attorney Laura Vaughn called psychiatry a "form of abuse."
"That is their right to believe that psychiatry is abuse," she said. "It's Lisa McPherson's right to believe that, and to not engage in it if she doesn't want to."
Two of McPherson's closest friends in the church insist she would not have wanted more traditional treatment.
"She would not have wanted to be treated by a psychiatrist. I know that without question," said one of the friends. "I don't care what the circumstances were. She would not have wanted to be treated by a psychiatrist."