Thinking about Indy's ending... even the end of Raiders is not so explicit. Does the power of the Ark let Indy and Marion live just because they "closed" their eyes? Or because the Ark "knows" who are the good and the bad people?

This alien obviously knows that Spalko is a bad person, he can read her mind. So as a "gift" he confronts her to the horrible things past and future done in the name of communism (newsreels). And bam! head explodes.

It's not that bad. I'm open to others ideas, but for now it's the best one. It's no radical change from the movie though, but it adds a bit of an explanation about what happens.