Switching to OpenGL2 rendering backend was indeed a big change, but did you have to update anything to work specifically with QVTKOpenGLWidget? My understanding is that QVTKOpenGLWidget and QVTKOpenGLNativeWidget are drop-in replacements.
QVTKOpenGLWidget may have been developed later, but it is not better than QVTKOpenGLNativeWidget - it is only for very special cases: when stereo rendering is needed and your application can comply to a number of restrictions. The conclusion of lengthy discussions on this topic is that QVTKOpenGLNativeWidget is what people should use by default. Current class names misleading but not changed to prevent further frustration of application developers.