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The incident pertaining to the case took place on the night of March 15.
The woman, who became pregnant, attempted suicide and is currently undergoing treatment at Konni Medical College Hospital.
Santhosh allegedly asked the mother to remain inside the church and pray while he spoke to the girl privately.
The accused is already under judicial custody in connection with the first complaint.
The accused have been identified as Fousiya (43), a cook at the school and a resident of Edneer in Badiadka panchayat, and Shafeer K M (51), a cleaning staff member from Chala in Kasaragod town.
The 2016 case involved the brutal rape and murder of a 30-year-old Dalit woman in Perumbavoor, which led to widespread outrage and the arrest of Ameerul Islam.
The Fast Track Special Court judge Anju Meera Birla found Shainu, a native of Vettakallu, Thiruvallam, guilty and imposed a fine of ₹30,000.
The accused, Yadu Girish, a native of Thanniyam in Thrissur, was arrested on January 5.
The Court emphasised that the alleged offence did not progress further solely because of the intervention of third parties and therefore could not be categorised as mere preparation.
Based on her complaint, the Melparamba Police booked the 22-year-old man.
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