The judge lifted the stay that had been blocking the program's termination.
The employee works as a data analyst at City Hall, and his arrest has sparked outrage.
Oscar Solarzano was arrested after allegedly stabbing another man in the chest in north Charlotte Friday evening.
The U.S. is pausing all immigration applications, such as requests for green cards, for people from 19 countries.
The decision could potentially allow thousands of immigrants who have been subject to mandatory detention to be released.
Some activists fear that the crackdown in Charlotte could reach other parts of the state, including the Triangle.