The woman and man belonging to different communities had allegedly eloped from Bijopur village under Chapar police station in the district on November 3, they said.
The woman, who is once married, has claimed that her husband had divorced her and she eloped after that and got married with her lover, they said.
The woman had approached the Allahabad High Court seeking police protection for herself and her partner. The high court had ordered Chief Judicial Magistrate to record the woman's statement after her medical examination.
The trouble started today when the woman was taken to the district hospital here for medical examination before being presented in the local court, police said.
Angry over the alleged elopement, people of a community pelted stones outside the hospital and tried to block road at Minakshi Chowk here, they said.