Relatives of the slain villager and the girl pelted each other with rocks, broke shop front windows, and shot bullets into the air before police restored calm to the southern village of Dayrut.
The clashes erupted after four relatives from the girl's family had their detention extended by police investigating their involvement in the murder.
Henry Atallah was shot dead while waiting in his car on Oct. 18 in the nearby village of Attaleen, near the southern city of Assiut.
According to police, the murder was prompted by rumors that Attallah's son had taken intimate pictures of the girl and distributed them by mobile phone and CD.
Egyptian Christians, known as Copts, make up an estimated 10 percent of Egypt's 78 million people and generally live in peace with the Muslim majority although they complain about discrimination.
Clashes have erupted in the past in Egypt's impoverished south over the issue of building churches or just escalated from ordinary marketplace squabbles.