Even low level federal officials have an independent duty not to violate peoples' constitutional rights. They can be held personally liable for violating clearly established constitutional law, and following administration policy is not a defense. Usually the "clearly established" part protects the low level folks, but here you could see CBP line agents being held personally liable for excluding green card holders.
On top of that, the AG has additional obligations as an attorney. An attorney must sign her name to every legal argument she makes to the court. She may not permit a non-attorney to override her legal judgment. Here, the AG did not hold a press release discussing the politics of immigration. She told her subordinates not to make legal arguments defending the order--arguments she would have had to sign her name to. It is absolutely an exercise of professional judgment, not policymaking.
Of course Trump can fire her for any reason. But the public is also entitled to draw reasonable inferences from those actions.