Humans are funny, they think in sometimes seemingly illogical and nonsensical ways.
Humans fight, being ready to die, but whent the soul has departed and the person is now merely a corpose---the remains now composed of the five elements minus the soul which gave life to it---they still want it to be treated in a certain fashion. There is a certain closure, a certain dignity and a certain drawing of curtains that is associated with it. Many armies (some more than others) spend considerable effort to retrieve the dead bodies. They sometimes take additional casualties just to retrieve the dead. Some of them are from nations well known for their pragmatic, practical & logical modern streak. That is just human nature.
Regressive and brutal regimes understand that it is not merely enough to ki11 someone, but it is also important how that end comes about. I am not talking of torture (which is another ba11 game altogeter). That is why the British chose to blow dozens of Naamdharies in the Punjab by tying them to the mouth of cannons, rather than simply shoot them, which would presumably be quite cheap and less messy. (report of that massacre indicated that flesh was flying all over the place). This grisly end was designed to cause the living to think in a certain way. Bhagat Singh did not want to be hanged, he wanted to be shot, because that is an end which respectable soldiers get. British obviously wanted to hang him like a common criminal, to deligitimize him.
All faiths lay down conditions how the dead must be disposed off, often based on theological reasoning. This method of disposal has important consequences. In the context of RoP, there is an antipathy to being burned. I have already pointed one example from Indain history. RoP considers disposal by fire to be "Napaak". (There is a reference to a Mughal General Sulhi Khan, who had come to hurt the 5th Sikh Guru, whose horse bolted and dashed into a brick kiln oven and was burnt alive. He was referred to as meeting a "napaak" end in the Sikh scriptures.) Of coure, RoP has come a long way, it has enough ideoological flexibility that it will not stop dead on its tracks. I am under no illusion that atankvaad will suddenly come to a stop by burning. As someone pointed out, fatwas can be purchased on eBay for dime a dozen. But still it is a low-cost no-risk option.
As strange as it sounds, but the relatives of jeehardies who attain shahadatdom in India also want a certain closure. They, since they are human too, feel sorrow, anger, grief. As part of that process there is a certain closure they seek. In the dying there is a certain element of a curtain being drawn and an act of closing a chapter. As heineous the act of their relative, they still seek a respectable end and respectable treatment of the remains of their loved ones. This, after all is also a need. GoI, or IA can decide to satisfy that need, or deny it. It can deny it in ways that puts burden of shame and ignomony on the individual and family (and takes away respectability). It is after all war, and this is a small but important pshychologial strike that we can make. It causes the other Ammi and Abbu's a future Jeeahardie to pause, they will realize that that their loved Azhur will not only give up his life, but will not get a proper end to his body once he steps into Indian soil.
IA and GoI tends to treat fallen atankvaadis as pseudo soldiers, which is what the TSP'ians want them to be thought as. We should be dispelling that illusion by denying any Geneva convention-like treatment to the remains. I am, of course, not suggesting putting pigs meat etc, because this us unecessarily inflamatory. That suggests a purposeful, deliberate and quite-frankly desperate humiliation; we should be doing only an absent minded lack of interest in the faith and disposal techniques. Also, what is wonderful is we dispose these guys just as we dispose our own dead, but with an absence of respect.
Shiv, your points are not invalid. Burial does preserves genetic material. Do we then bury the "Hindu" or "Budhist" atankvaadis too? I am pretty sure we don't bury them. I do not think we are motivated by forensic considerations. One question, do medical colleges need a fully intact cadaver? Can they not take in partial caddies?
Perhaps I should stop and not flog a dead jeehardie any more!!!
@Vikas Raina: Thanks for the welcome. Feels nice to be posting after a long hiatus.
India is striving for a larger than life role in Afghanistan; the effort is mainly motivated by the instinct to acquire a launching pad to destabilise the western stretch of Pakistan. Incontrovertible evidence of Indian involvement in Balochistan 
and many other incidents of terrorism in various other parts of the country support the notion that India is once again on a Pakistan squeezing spree.
