I found some of the arguments about Indy 4 to be overly exaggerated.
Really? The Ark of the Convenant, Vodoo Dolls, The Holy Grail and people think aliens is too much of a stretch?
I thought this exchange did a good job in fitting aliens in with judaism, christianity and hinduism:
[looking at the odd shaped human skulls]
Mutt Williams: Why'd they do that?
Indiana Jones: To honor the gods.
Mutt Williams: No, no, God's head's not like that, man.
Indiana Jones: Depends on who your god is.
Really, the main drive of each Indy film is a religious artifact. So I see no problem in having aliens as a religion. Hell, people exist who worship aliens. Like Tom Cruise.