It means whatever Nunnaly is going to do is going to get Kallen out of that cell.
She could possibly pardon her, but I doubt that will fly with anyone, and Nunnaly is a powerless leader really. She might take her to Charles and ask him to pardon her, which results in Charles Geassing her into thinking she has always been a spy or something and setting her off to destroy the Black Knights from within. Or Geassing her and making her a Knight of the Rounds to taunt Lelouch.
Another, and in my opinion, more likely option is that Nunnaly is trying to make Kallen both free and untouchable by the rest of the powers within the Britannian military by making Kallen her knight.