I was not aware of Hoodbhoy's distorted thinking and very scant knowledge of history.
THE TWO NATION THEORY is founded in the Qur'an.
2:256 (Although this Message has been sent down by the Almighty) there is absolutely no compulsion or coercion in Religion. The right direction has been made distinct from error. So, whoever rejects false gods (such as the clergy, human ‘authorities’) and attains conviction in God, has grasped the Unbreakable Support. God is Hearer, Knower. [No compulsion in matters of religion - This Rule shall have no exceptions since Right has been distinguished from Wrong. 2:148, 2:193, 2:256, 4:88, 5:48, 6:104, 6:107-108, 7:177-178, 10:99, 12:108, 18:29, 22:39-40, 27:80-81, 39:41, 56:79, 73:19. At-Taaghoot = Those who, in rebellion to the One True God, claim to have Divine powers or try to portray themselves as His representatives = Sufis, mystics, priesthood, clergy, tyrants. Tagha = Rebellion. Idols of stones cannot rebel and therefore, they cannot be At-Taaghoot]