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I pardon to differ here, no cricket board is independent entity. Every board is controlled and monitored by government bodies. So its not true to say that BCCI is independent entity. India is not playing with Pakistan even before 26/11 attack, if you see current government stance they have zero tolerance towards Pakistan. IPL franchise and BCCI not allowing Pakistan is just because of Indian government pressure. Franchises will love to involve Pakistani players as they have world class T20 players.
The government did intervene India having any cricket series after the terrorist attacks and from what i remember only cricket is barred and the rest of the sporting events are taking place as usual between the two countries. BCCI is an independent body just like any other sporting body. For example New Zealand cricket board was willing to travel Pakistan and they were in the ground but the government called the players back citing security reason.
So any sporting body representing a country can be dictated by the government policy but the functioning is independent of government intervention.