The girl was raped in July this year by Nayoom (19) after which her father lodged an FIR against him, they said.
He was under judicial custody since then.
The accused family members had also threatened the girl with dire consequences, police said.
The girl's parents alleged that the victim was strangulated to death and later hanged on a hook while they were away from the village yesterday.
A murder case has been registered in this connection.