I don't have the Indy DVD's, but it sounds like Spielberg and company have changed their tune about TOD since the original making of doc aired on PBS around 1984. He certainly had no qualms about it being darker at the time!
About the only thing he was squeamish about back then was the sacraficial victim being lowered into the lava. ILM's puppet stunt double writhed in agony a little too well in the dailies, and Steven had them obscure most of the effect with added flames.
It's sad that documentary will probably never see an official video release.