But he added the charges were made necessary by the unique circumstances surrounding the 1995 death of Scientologist Lisa McPherson while in the care of church staffers.
"This is the first time in my 23 years that I've seen anything quite as bizarre or disturbing as the way this decedent was treated," Pinellas-Pasco Assistant State Attorney Doug Crow said.
His remarks came during the first of many hearings in a case that began Nov. 13, when the Church of Scientology's Clearwater branch was charged with abuse of a disabled person and practicing medicine without a license. A trial has been set for March 6 next year, and is expected to last two to five weeks.
Crow was responding to statements by Scientology lawyer Sandy Weinberg, who suggested to Chief Judge Susan F. Schaeffer that the charges by Clearwater police were "religiously motivated." The department has investigated Scientology off and on since the church made Clearwater its spiritual headquarters in 1975.
"There must be a reason for (the prosecution)," Weinberg said. "We don't think it's based on the facts."
Never before in U.S. history has a church been charged for the actions of its members, Weinberg said. He said the Catholic Church, for example, has never been held criminally responsible for the sexually improper actions of some priests.
McPherson, 36, died in the care of church staffers who watched her for 17 days inside the Fort Harrison Hotel, a Scientology retreat in downtown Clearwater. She was taken there to recover from a mental breakdown because Scientology strictly prohibits its members from receiving psychiatric care.
The church contends the staffers were conducting an "introspection rundown," a Scientology procedure in which people presumed psychotic are placed in quiet, dark isolation to calm down before receiving Scientology counseling. McPherson was highly combative during much of her stay.
Weinberg called the "introspection rundown" a religious practice that is protected under the First Amendment to the U.S. Constitution.
But Crow argued there was nothing religious about some of the methods church staffers employed during the isolation, including forcing food and medicine down McPherson's throat, sometimes with a large syringe as they held her down. Crow also noted that she tried to fight her way out of isolation, that her non-Scientologist relatives were never notified, and that she was taken to a hospital too late.
In documents filed this week, the church concedes the actions of its staffers were negligent and against Scientology policy. They were practicing a constitutionally protected religious rite, the church says, they just didn't practice it correctly.
Judge Schaeffer signaled she would look favorably on the religious argument as both sides prepare for trial.
Many religions believe in the laying on of hands to cure people, Schaeffer said. "In fact, I grew up in one." The judge said she was raised in the First Church of God. She said her mother claimed to have been spiritually cured several times.
Crow countered, saying there were many ways to get McPherson the mental health care she needed without violating the Scientology's religious beliefs. One would have been to take her to a doctor sooner, he said.
The church took no steps to rule out the possibility that McPherson's problems were physical, he said.
"They are making diagnoses that they're not entitled to make," Crow said. "These are people who have no training to make those decisions."
But the judge cautioned that Crow's argument could run counter to the Constitution. "I don't want to be trying a case that's going to involve stepping on someone's religious beliefs," she said.
McPherson, it could be argued, consented to her treatment at the Fort Harrison by virtue of belonging to the church, Schaeffer said.
Crow countered, saying: "Neither individuals nor corporations have a religious right to engage in practices that violate criminal law."
The hearing offered a preview of the months ahead as the church mounts a defense that will revolve around a variety of constitutional issues. Sitting in the courtroom near Scientology's Los Angeles-based executives was the church's top First Amendment lawyer, Eric M. Lieberman of New York.
The hearing ended with a minor legal victory for the church.
Weinberg said the charges were vague and did not make clear how the alleged crimes were committed. Schaeffer asked Crow to craft a document that would clarify.