Justice R M Chhaya passed the direction on Maria's application seeking relief after her long-term visa expired and her application for extension was rejected.
The judge asked her to file an application for Indian citizenship by January 14. If no such application is filed, then the authorities can deport her to Pakistan, the court said.
The Union government must decide her application by February 15, the court said.
He got bail in November 2014 to marry Maria, who had come to India from Pakistan on a long-term visa. The couple has a one-month-old daughter.
The state government rejected her application for visa extension and asked her to leave the country by January 8.
Maria, in her petition in the high court, argued that the state government does not have the power to reject her application based on the adverse opinion of police.