I don't think it matters a jot if GR9 is cheaper to operate than GR4. With 2 front line squadrons left, and the Navy's oft-mentioned need to keep practicing carrier based ops, the force is too small to sustain any sort of operation now.
If you want to keep UK fast jets in Afghanistan, you keep the GR4 in some capacity. In any terms, trading a deployable force that's doing the job as we speak for one that seem to exist purely to keep the FAA current on carrier ops seems a bit silly.