The main reason is that what Khomeini cited is exactly what Prophet Mohammed had said. Khomeini was following Prophet's words to the verbatim. Religious leaders are considered as supreme in Islam. Prophet Mohammed was a priest, law-giver, ruler, arbiter etc. Remember Islam is defined by practice of a class of creed systems.
Political leaders using religion and religoius men indulging in politics is well-known.
Unless there did exist such a deep divide in views, thoughts, practices, beliefs etc. and etc., the British themselves would not have been successful. The creation of Pakistan, to protect the Moslems, is another hoax. What Jinnah knew what that the Moslems were once ruling before the British defeated them. The centrist and absolutist form of orthodoxy in the Islamic fold forbade the Moslems from taking advantage of the Western style of education that the British bought with them. The mullah and the clergy dissuaded the Moslems from taking the advantage of the British system of education.