At issue: Both prosecutors and two of the three judges were replaced Sept. 1.
"This is a serious and really unacceptable scandal, concerning such a huge case," Orhan Kemal Cengiz, a lawyer for the victims, told Open Doors News (formerly Compass Direct News).
Umut Sahin, from the legal committee of the Turkish Association of Protestant Churches, told Open Doors that the replacement of the prosecutors has impacted the case in an "unbelievably negative" way.
During six days of hearings, "the new prosecutor did not utter a single word for the whole six days!" Sahin said.
Turkey's Council of Judges and Prosecutors, however, told Open Doors that the reassignment of the prosecutors and judges was a routine transfer following recent legal reforms.
The five suspected killers who were apprehended in 2007 at the scene of the crime denied any links with an alleged military plan to overthrow Turkey's ruling Justice and Peace Party (AKP), an Islamist bloc led by Prime Minister Recep Tayyip Erdogan.
"We went on an expedition on behalf of Islam on our own to accomplish this event," defendant Emre Gunaydin told judicial officials, as reported by Open Doors.
The 761-page indictment, however, alleges the five accused murderers were not isolated extremists, but rather part of a so-called Cage Action Plan to undermine the Islamist-leaning government.
During the hearings in early September, six of the accused soldiers testified that the local gendarmerie, sometimes aided by police and secret intelligence officials, had been monitoring the handful of Christians in Malatya and paying informers to collect data on their activities. The gendarmerie is a law-enforcement arm of Turkey's military with jurisdiction outside of cities and towns.
Following the murders, according to Open Doors reports, gendarmerie officers tapped the phones of the victims' families, lawyers and judges in the case and gave false testimony and documents, attempting to tarnish the murdered Christians by linking them to illegal groups like the Kurdistan Workers' Party.
"I was obeying orders conveyed to me within the command-chain hierarchy," Sgt. Adem Gedik told a judge, according to Open Doors.
Among the suspects are retired Gen. Hursit Tolon, who was named a prime suspect behind the killings; Col. Mehmet Ulger, who commanded the Malatya gendarmerie at the time; Ruhi Polat, a theology instructor at the local Inonu University; and Ilker Cinar, an intelligence agent assigned to falsely convert to Christianity, infiltrate the Turkish church and then publicly "reconvert to Islam," denouncing Christians as threats to national security.
"Is it possible that the AKP government is uncomfortable with the conclusion of this case?" columnist Orhan Oguz Gurbuz asked after the initial hearings in a Sept. 16 column for the Turkish publication Today's Zaman. "The government must address these doubts and questions. Otherwise, it will undermine its own legitimacy and the pluralist/democratic identity that it has relied on since the beginning."
Susanne Geske, widow of Tilmann Geske, still lives in Malatya with her children. She told Open Doors that the nation should learn the truth about the murders, recalling previous cover-ups by Turkish officials.
"This trial doesn't change anything for our family," Geske told Open Doors. "But it can change things a lot for Turkey."
The alleged Cage Plan conspiracy centers around a compact disc found last year at the home of a retired naval officer. A group of 41 naval officers were to carry out a campaign of assassinations against Turkey's non-Muslim minorities to portray the country's Islamist government as unable or unwilling to protect non-Muslims.
The plan included "operations" for the murders of the three Christians in Malatya, the 2006 assassination of Catholic priest Andreas Santoro, and the 2007 killing of Hrant Dink, the Armenian editor-in-chief of the weekly publication Agos.
"It wanted to send a message that the AK Party government was radically Islamist and makes targets out of Christians," columnist Orhan Oguz Gurbuz wrote in a Sept. 16 column for Today's Zaman.
Hearings on the case are scheduled to resume Nov. 12.