So my basic question still remains - If a Soldier protects the nation - who is protects the soldier ?? APPARENTLY NOBODY !!

The points are very simple. An FIR is mandatory wherever there is an untoward incident and anyone can file it; even a bystander. The Army is required to file one for every incident procedurally.

The second is that an FIR and a charge are two different things. A charge is made after investigation and after sanction from the Central Government. As you said the provision is applicable to all on Govt duty.

You are very right as regards the Govt permission being required to prosecute any Mil Pers for any acts of  commission/omission  in the line of Duty - which is true for ALL Govt servants , ( and not only the Armed Forces ), be it IAS, Police et al.

The point here is regarding the FIR stage itself  viz filing of the FIR itself , against an Army Personnel for acts arising out of duty-bound actions.     

To  the best of my  knowledge,  Protection at that stage viz against an FIR  also exists under AFSPA -- and as also quoted by the lady lawyer of the major  - for the simple reason  that investigations under an FIR itself can very easily be turned vindictive and biased, besides harassment and  psychological pressure by way of prolonging the investigations and multiple/infructuous summons. 

And mind you, AFSPA is expressly meant to enable Army discharge its duties effectively in HOSTILE domestic areas viz when operating against Own Population gone rogue , violent or truant, much beyond the capabilities of other law-enforcing agencies and even Army with its limited powers in aid to civ auth.

The protection from Prosecution ( needing Govt permission ) is an Umbrella protection for ALL Govt servants, which  comes ONLY  AFTER police makes out a viable case with evidences ( consequent to Invetigations based on FIR ),  frames a  legal charge sheet and files a case in a Court for further/final prosecution.

Hence here the moot question is, if a mil person or a mil cdr  charged  / assigned  with  an order to quell a  violent mob has to  constantly worry about an Impending   FIR or is fully aware that the Govt will not back his bonafide actions,  HOW on earth will he discharge his duties  faithfully ??  

And at least on my own personal behalf, I am definitely sore that the soldier or his family has to fight for this justice in his private/personal capacity and it is neither the Army nor the MoD who filed this appeal to H'ble SC against the Mehbooba Mufti dispensation. 

(( ** It is besides the point and a very insignificant consolation that there WAS a Central Govt counsel in SC hearing day before yesterday, who in principle supported the Maj Aditya's plea )).

The very fact that the SC has ' stayed " the FIR , and now apparently  Mehbooba Mufti  too being on back foot  ( lamely saying that the Major has NOT been DIRECTLY indicted - only named as the  Officer in charge of Army convoy ! ), itself indicates that the FIR is indeed is not above board.

Many policemen being hounded by the legal process for doing their duty. This happened in Punjab , for many years, with cases against policemen who had killed terrorists in the line of duty.

One set of events have been rather Intriguing and  disturbing - the issue of FIR against the Army Personnel in J&K, wherein civilian  deaths are involved --  even if he is a Violent Stone-Pelter  or a Terrorist  . 

however, the very fact that the H'ble SC has  put a stay TWICE  in last few weeks on any such investigations under this FIR and on any further action against the Army, raises many a fundamental issues. 

In fact, most of the Legal people have always maintained that an FIR can be filed against an Army person  (( for doing what he did in his line of Duty and especially under AFSPA and Disturbed Area kind of conditions )),  ONLY with the approval of the Central Govt viz the MoD, in case of Army.

MILLION  DOLLAR  QUESTION ~~ Basically, WHO should be fighting this case (  to safeguard the  interests of the Army and its personnel and its assigned charter vis-a-vis  actions necessary to implement this charter in J&K ) in the Court -- the private Individual ( father of  the Major , foe example,  in this case ), or  the Army as an organisation  or the  system viz the MoD ?? 

Does not the Onus lie with the MoD to protect the interests of the Army, who  are the ones to have thrust/deployed and ORDERED the Army in J&K in the first place , and  has  tasked the Army to deal with Violent Militancy ? Have they not any responsibility/accountability in their capacity as the Ordering/Controlling  Authority ?

An innocent and Plaintive  Question comes to my mind -- Are FIRs lodged against each and every Police personnel involved in the many a  daily   law & order shoot-outs and encounters which take place in our urban and rural areas -- killing  robbers, the dacoits , criminals etc ,of genuine & routine killings that take place at the hands of Police - are they too hounded by the so called same Criminal Procedures , the Public and the NHRC types ? They too are doing their duty, No ??

Are  the Policemen who shoot dead a a rogue chap going on a killing spree in American Schools also booked/persecuted  under an FIR ( or a similar stuff ) in US or any other country

So my basic question still remains - If a Soldier protects the nation - who is protects the soldier ??  APPARENTLY  NOBODY !!