The party's politburo member said instead of celebrating inter-caste and inter-community marriages as "symbols of Indias open and liberal approach", there was a campaign against them.
"The NIA is on a fishing expedition having already interrogated 89 such couples in Kerala," Karat said in the latest issue of party organ 'People's Democracy', while referring to the Hadiya case.
She was critical of the central agency's role in probing such marriages, referred to as "love jehad" by Hindutva forces.
The underlying assumption, she said, was that Hindu women who married Muslims had "no minds of their own".
"Her (Hadiya's) case reveals how deeply the current climate created by sectarian ideologies based on a narrow reading of religious identity has pushed back women's rights to autonomy as equal citizens. From the government to the courts, to the strengthening of conservative and regressive thinking and practice, it's all out there in Hadiya's case," Karat wrote.
"It was the courage of her conviction that stood out. She wanted to be treated as a human being. She wanted her faith to be respected. She wanted to study. She wanted to be with her husband. And, most importantly, she wanted her freedom," the former Member of Parliament said.
Karat said she appreciated the Supreme Court "for not allowing itself to be converted into a khap panchayat" and charged the NIA counsel supported by the legal counsel of the Central government with portraying it as a case of "indoctrination and brainwashing in a conspiracy of 'love jehad' which they claimed rendered Hadiya incapacitated and invalidated her consent".
The Left leader emphasised that Hadiya's case brought into focus the right to practise and propagate the religion of ones choice under the Constitution.
Karat expressed the hope that the apex court would "act in a way which strengthens womens rights unencumbered by subjective interpretations of tradition and communal readings of what constitutes national interest".
The 24-year-old Kerala woman had converted to Islam, changing her name from Akhila to Hadiya, and married Jahan. The marriage was challenged by her parents in court.
Jahan moved court after their marriage was annulled by the Kerala high court and against the high court courts order directing the NIA to probe the case.
The Supreme Court last week allowed Hadiya, till now in the custody of her parents, to resume her studies at a homoeopathy college in Salem, Tamil Nadu.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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