On Friday in the NSW Supreme Court, Justice Elizabeth Fullerton said that she was legally unable to deliver a verdict of guilty or not guilty because Church, 53, had died on Thursday.
"I regret that the trial proceedings have concluded without verdict. I hope the members of the public and more importantly Ms Smith's family members and her many friends understand the position as I'm obliged to abide by it as a matter of law," the judge said.
In evidence from the police handed up to the court, Church was found dead at his home by detectives from the northern NSW town of Inverell on Thursday.
The death was not suspicious with Church believed to have taken his own life, Justice Fullerton said.
With the death of the accused, the trial ended, a conclusion that the judge acknowledged would be difficult to those who knew Ms Smith.
"The law simply does not allow me to return a verdict, to publicly announce it, or to publish the very lengthy reasons which were ready to be published this morning," she said.
Church, a NSW horse farrier, was charged with the murder of his 23-year old lover on the NSW Central Coast on August 19, 2012.
He pleaded not guilty in January this year and had been released on bail. The case was brought in a 68-day judge-alone trial which concluded on May 24.
Ms Smith's body has never been found but her abandoned car was discovered at Tuggerah railway station more than a month after she vanished.
The Crown had alleged Church killed Ms Smith after she told people she was pregnant to him and because he wanted to save his new relationship with Belinda Lees.
But the defence contended other scenarios could not be ruled out including that Ms Smith's violent ex-boyfriend, the late Craig Elkin, could have been involved or that she disappeared on purpose.
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