Are you trying to calculate the surface latitude/longitude of the spacecraft? Based on your code samples I think that's what you are really trying to get to. To do that you need to take into account the ellipsoid. Your calculation is calculating geocentric latitude/longitude, which is more akin to spherical coordinates locked to the ECF frame. To get the geodetic lat/lon you can do something like this:
Frame ecf = FramesFactory.getITRF(IERSConventions.IERS_2010,true);
OneAxisEllipsoid earth = new OneAxisEllipsoid(Constants.WGS84_EARTH_EQUATORIAL_RADIUS, Constants.WGS84_EARTH_FLATTENING, ecf);
GeodeticPoint satLatLonAlt = earth.transform(pvCoordinates.getPosition(), FramesFactory.getEME2000(), date);