BCCI is independent entity, ICC doesn't allow government interference in cricket not even indirectly. Zimbabwe board faced a ban because of this. Banning Pakistani players from the IPL wasn't Gov's decision but BCCI and franchise, especially franchise considering BCCI allowed Pakistani players to put their names at the auction but after 26/11 terrorist attack, every franchise boycotted them for the right reasons.
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.