Based on the information available to you, you absolutely did the right thing going over her head. I sorta helped run a smallish but still publicly traded (NASDAQ) company based in Burlingame for a number of years. Lived up here--well, actually, sorta lived on the airplane--but still worked in the Bay Area all the damn time. CA employment law is super strict. You have a responsibility to try to not waste corporate funds. even if you could clean this up at end-of-year, why not do it right the first time? You are a great employee. I used to love it when employees came to me with this sort of thing.
We had an old saying when I was still seeing patients for a living, before the laser company and everything. The saying was:
Poor planning on your part does not necessarily constitute an emergency on mine.
You should get your CFO a tee shirt with that on it. You could put a cute kitty cat underneath it...
Okay, well, maybe get the shirt for you.