Q What do you do when a higher-up asks you to do something that effectively circumvents a written policy, while she is also providing you with a rationale (rationalization?) for why it doesn't do just that?
A Is it a choice between keeping your job or living with your conscience, or is there something in between?
The inner game
This may be an emotional issue for you, tapping into your sense of right and wrong. Acknowledge your feelings in the situation so that you can give them their proper place in planning your reaction, rather than acting impetuously on them.
Now take a dispassionate look at what you're being asked to do. Apart from being out of alignment with policy, what do you think about the action? Is it illegal, unethical, or immoral? Would you think it was a good idea if the policy were different? Draw your own conclusions about the act, apart from policy.
Consider the policy itself, particularly determining if the "higher-up" in question has the authority to change the policy. If so, this may ease your dilemma.
Finally, go inward. People generally have a good gut feel for what they should do. What messages are you getting from inside? What would you advise someone else in this situation?
The outer game