First of all, you can't get the focal length in metric coordinates from the camera calibration. fx and fy are given in pixels and contain both the (metric) focal length of your camera as well as the metric size of your pixel-sensors. (a smaller sensor with a lager distance from the aperture creates the same image). If your pixels are not square, fx and fy differ (although they are very similar for every camera I used so far). So if you need a single focal length somewhere, just use the mean of both values.
