It isn't.
In the prior Indiana Jones movies, the Occult is real. They aren't science fiction stories, they are stories about what the world would be like if the basis for Christianity/Islam/Judaism were true.
Crystal Skull is all about aliens, and completely denies the reality of the Occult by explaining everything as technologically advanced aliens.
Crystal Skull doesn't deny the occult. I can name more than one series where magic and aliens/science-fiction coexist.
Also, Indiana Jones isn't about what the world would be like if Christianity or Islam were true, they're throwbacks to old adventure serials that would be aired in movie theaters during the 40's and 50's.
Finally, it should have been patently clear that aliens would be involved in the movie right from the title. "Crystal Skull". The Crystal Skulls are believed by many people to be alien artifacts (it's not true, the Skulls are confirmed fake, but people are dumb and believe it anyway). They're a core aspect to the Ancient Aliens idea. That's like watching Last Crusade and complaining about the overt Christian overtones.