An RFE/RL correspondent in Kara-Suu reports that a dozen security service officers guarded the morgue in the nearby city of Osh before the family received the bullet-riddled corpse.
Authorities closely watched the proceedings as more than 3,000 mourners gathered at the imam's house, local police said.
'They Were Frightened Of Him'
The crowd carried Kamoluddin's body through the streets of Kara-Suu to the city cemetery chanting, " God is Great!" ("Allah Akbar!") and "Martyr!" ("Shahid!").
The mourners say Kamoluddin died in the service of Islam.
Kamoluddin's son, Rashod, has accused Kyrgyz authorities of a campaign of harassment against his father.
"[First] they tried to imprison him, then the people protested and they (authorities) were frightened. Now they've put a gun into his hand and shot him dead," Rashod said. "He is a martyr. They got rid of my father. They were frightened of him because he had 20,000 or 30,000 followers. I will meet with my father in paradise."
The 53-year-old Kamoluddin was killed in a joint Kyrgyz-Uzbek security raid in Osh on August 6 along with two men whom authorities have described as Tajik citizens.
Authorities say Kamoluddin was a "terrorist" member of the violent Islamic Movement of Uzbekistan (IMU). They have implicated all three of the dead men in a deadly border incident in mid-May, and say they were planning further attacks before they died in a firefight during a "counterterrorism" operation.
Kamoluddin was outspoken in his belief that members of another banned group, Hizb ut-Tahrir, should be allowed to worship in his mosque. But family members rule out any ties between terrorists and the slain imam.
Abdulloh Kamalov, the imam's younger brother, told RFE/RL's Uzbek Service that Kamoluddin died "because he spoke the truth in the mosque." His brother "didn't get involved in politics," Kamalov said.
Kamoluddin was publicly critical of Hizb ut-Tahrir's ideology. He said he believed they were "misguided" but should not be excluded from prayers, citing the example set by the Prophet Muhammad.
Hizb ut-Tahrir followers were among the mourners on August 7.
"We can say this after his death: [Rafiq Qori Kamoluddin] was not a member of Hizb ut-Tahrir," one of them told an RFE/RL correspondent in Kara-Suu. "Yet he was a genuine Muslim."
Kamoluddin had been questioned by authorities and even briefly detained by Kyrgyzstan's security forces in the past over his suspected links to militants.
National ombudsman Tursunbai Bakir-uulu defended the imam's position on Hizb ut-Tahrir in an interview with RFE/RL's Kyrgyz Service on August 7.
"A mosque is Allah's house, where anyone can come and pray. Hizb ut-Tahrir members or others may have come [to Kamoluddin's mosque]. But it is not written on their foreheads that 'This one is a Hizb ut-Tahrir [member],' and 'That one is an extremist.' Only those who want to pray come to mosque. It is up to the security service, not the imam, to figure out who is coming and who is a terrorist."
The funeral took place peacefully, with no violence reported.
But several mourners called authorities' actions a crime. Statements from some followers suggest tensions could remain high in Kyrgyzstan's volatile south.
"The people's hatred and anger is very strong right now," said Ahmad Jalilov, who was present for the funeral. "We knew [Kamoluddin] as a person who called for truth. We witnessed how he spoke only the truth about Islam and called on all Muslims only to [do] right and good things. We will wait for official information from the government."
Another mourner demanded a thorough investigation into the killing.
"We are not going to carry out any kind of investigation ourselves," he said. "We demand that the government bodies -- financed from the state budget and by taxpayers -- find those criminals [responsible for Kamoluddin's killing]."
One of Kamoluddin's relatives described Kamoluddin's death as a part of a government campaign that is targeting Muslims and vowed revenge.
"God willing, we are going to find out who, when, and for what purpose this crime was carried out," the relative said. "Revenge will be a response to this inhuman brutality. What's significant is that Muslims' lives in Kyrgyzstan are also in danger. Imprisonment or detention without trial has been a practice before. Now, direct murder and shootings have begun."
Ombudsman Bakir-uulu also highlighted the importance of illuminating the circumstances of the imam's death.
"This person devoted his whole life to serving a religion," Bakir-uulu said. "His authority and reputation were very high -- not only in Kyrgyzstan, but also in Uzbekistan, Tajikistan, and Iran. Therefore I believe investigators should find out whether the shooting was necessary and whether [Kamoluddin] had a weapon."
Bakir-uulu said his office will conduct its own investigation.
In the meantime, Kyrgyzstan's security forces are likely to keep a close eye on events in the south to ward off any possible backlash once the findings are made public.