How would the discovery of alien life with advanced intelligence impact human-centered ideas of religion?

This is a follow up to this question regarding the likelihood of finding intelligent life elsewhere in spacetime.

Most human religions posit a creator who flung this vast Universe into being as a place specially designed for mankind to inhabit. How long would it take the Pope and the leading Mullahs and Muftis of Islam to come to grips with alien intelligence, particularly if they turned out to be advanced beyond man, and held religious beliefs at odds with sky-daddy based Earth religions?