Here we go again .... The only people who are going to win from such sensationalism are the Army (who must be pi55ing themselves laughing watching the other two Services tear each other apart) and the government (who are more than happy for Chiefs to resign because they know there's another yes man waiting his chance).
The following is all my personal opinion. The Tornado is up to the job in AFG. The Harrier is fast becoming a one trick pony and it needs time back home to regenerate and reconstitute its broader military skills i.e aviation from the carrier. If it was to stay out in AFG any longer there is a real chance that they would never regain deck currency period. And the beancounters would start to question the need for carriers in the present and in the future. So not only would the new carriers be delayed (another thread on that topic) but also rather than run on the current CVs, given we don't have enough assets to keep the decks warm (because they're busy on ops) lets bin them early as well. And then we don't need JCA so lets buy more Typohoon (and that keeps BAE happy, and jobs in UK etc etc). So, again a personal view, bringing the Harriers home, and perhaps reducing the fleet size (I wouldn't advocate a complete disbandment for the reasons I've already stated) would support the procurement of the future carriers (again, which I believe we need) and JCA.
I also don't give a fig who crew JFH or JCA. Best person for the job.
I reckon the SofS will call his bluff - if CNS resigns then he will be replaced with a yes man who will have no choice but to support whatever proposals are put on the table (including those affecting the wider Navy, not just the FAA). If he doesn't resign then he will just be seen as a spoilt brat - I'll scream and scream until I get my own way. If he really wanted to make a point he should have had the balls to walk around the 5th floor, resign with no prior notice and then "leaked" his reasons/concerns to the press. His pension is both vast and secure and there will be all sorts of companies looking to welcome a man of such principles on to their board.
Of course, if he had nothing to do with the leak and it was done by a "well meaning" staff officer or civil servant then I suspect CNSs bacon and eggs will not be going down to well this morning!