To become an NCIS Special Agent again she would be required to be able to get a security clearance (this is why the position requires US citizenship). A pardon would not clear her of the underlying conduct that would effectively make getting security clearance with just a pardon to be problematic. She would have to have her record cleared... (i.e. she would lose her backstory that was put in place for being an intelligence operative). Basically, she would have to come in from the cold.