I think Chloe is doing her job by trying to stop Jack. If she hadn’t made the order for him to be pursued and escorted down then someone else would have been asked to replace her as Acting Director right away and the order would go out anyway. She is in a position to protect Jack. Ultimately she trusts him even though his actions put her in a very difficult situation. As long as she is running the show she will find a way to protect Jack while still doing her job. Jack would expect her to do exactly what she is doing.
