The deceased, Dharambir Kashyap was an eye witness in a rape and murder case of the girl in 2006, police said.
A case has been registered against nine people and three accused identified as Amesh, Ankit and Moji have been arrested in this connection, Atul Saxena, Additional SP told reporters here.
Meanwhile, enraged over the incident, villagers sat on protest last evening and refused to handover the bodies of Dharambir and his nephew Popin.
They later were pacified by senior police officials.