Paul McIntyre, 51, was refused bail over prosecution claims that people are too scared to provide information to police investigating events surrounding the brutal murder.
A judge was told graffiti in the Creggan area where Ms McKee was killed warns “any RUC touts will be shot”.
McIntyre, of Ballymagowan Park, is one of two men charged with rioting, petrol bomb offences, and the arson of a tipper truck on Thursday, April 18.
The allegations against him relate to disorder in the area when police came under attack by stones, petrol bombs and other missiles.
Four vehicles were hijacked during unrest said to have been orchestrated and led by members of the New IRA.
A number of shots were also fired by an unidentified gunman, one of which fatally wounded Ms McKee.
McIntyre is not charged with any offences directly connected to her killing.
But a Crown lawyer claimed he can be linked to the general disturbances through clothing and jewellery worn by one of the rioters.
Footage obtained from an MTV documentary crew shows McIntyre wearing a silver bracelet while in the offices of dissident republican-linked group Saoradh earlier that day, the court heard.
One of the masked men later seen carrying and throwing petrol bombs at police lines is wearing the same type of clothes and bracelet, it was alleged.
Opposing bail, counsel cited the potential for interference with the ongoing investigation.
Although more than 140 video clips have been received through a major incident public portal, no witnesses have emerged.
“Police say they believe people are frightened and won’t come forward,” the prosecutor said.“Historically it’s been difficult for members of the community, given the intimidation that has occurred in the area, and the graffiti is part of that same intimidation process.”
McIntyre’s lawyer stressed there was no allegation that he is linked to any threatening slogans or attempts to interfere with witnesses.
He also described the case against his client for the rioting charges as “weak”.
The barrister argued: “It relates to features seen on video footage that could be shared by hundreds, if not thousands, of people in the Derry area in respect of clothing and something sparkling on a wrist.”
Refusing bail for McIntyre to return to live in the same area where the rioting erupted four months ago, Mr Justice Horner highlighted the threats to prospective witnesses.
He said: “At the minute I consider the proper decision is to continue to hold the applicant in custody.”