The court directed the state government to provide adequate police protection to the couple.
According to the couple's lawyer, Sakshi and her husband Ajitesh Kumar were attacked by some persons, wearing black coats in the court room after which the judge asked the couple to remain seated inside the court room.
The judge also summoned the police officials and asked them to provide protection to the couple.
SSP Prayagraj Atul Sharma, however, denied that the couple had been assaulted.
Lashing out at BJP MLA Rajesh Misra, Justice Siddhartha Verma said that both his daughter Sakshi and son-in-law are adults and have a right to decide their life partners.
Sakshi and Ajitesh had reportedly eloped from their homes on July 3 and had got married at a temple in Prayagraj on July 4.
The couple remained on the run and on July 9, they posted a video in which Sakshi and Ajitesh claimed that they face a death threat form Sakshi's father and BJP MLA Rajesh Misra.
The couple said that the BJP MLA was 'unhappy' with their marriage as Sakshi was a Brahmin and Ajitesh a Dalit.
The MLA from Bithari Chainpur in Bareilly has, however, said he was not opposed to the marriage and his only concern was that there was a nine years age difference between his daughter and Ajitesh. The MLA said that the boy did not have a proper employment.
The couple later appeared on a news channel in Delhi in which Sakshi said that her brother and her father's associates had been hounding them.
( With inputs from IANS )