You make the case well but, while I also have some initial sympathy for your position, I'm not entirely on board. 'Raiders' is one of the very few movies I found so enthralling that after I first saw it in the movie theatre I turned around and bought a ticket for the very next showing and saw it again. If they had a third showing that night, I'd have gone to that one also.
First, on the merits of the argument:
Stealing a solid gold artifact to put it in a museum is a lot less villainous than stealing a solid gold artifact to personally profit by its possession, and even less villainous if the former be done in full knowledge that the latter was inevitable. I wish I could share your view that the artifact would be safest left alone, for that would be the least villainous, most righteous, of all. But was that even an option? if Jones knew Belloq wanted it--and knew he could get at it--would he be more or less villainous if he did nothing and let the artifact be taken, sold, and even possibly melted down for its gold?
On the age difference between Marion and Indy. The first time I saw the movie, I took Marion (the character) to be somewhere between her late twenties to early thirties. (Karen Allen, the actress, was just twenty-nine during filming). After she punches Indy she says 'I waited ten years to do that!' So whatever happened between them likely happened no earlier than when she was seventeen and likely not later than twenty three. So I took 'I was a child' to be euphemism. If the character of Indy was 35 in the movie, he would have been 25 ten years prior... (Harrison Ford, I just looked up, was about 39 at the time.) That would have made, at most, an eight year difference between them. I'm not sure it was entirely acceptable, but I don't think you can call it rape or pedophilia...
I have never heard the conversation you quoted involving Spielberg, Lucas and Kasdan and, indeed, find it very disturbing--and reflecting most poorly on Lucas. What a creep! Finding it '...amusing to make her slightly young...' Eew. But I don't see that in the final product. Like I said, when I first saw the movie I thought Marion Ravenwood was older and didn't get any creepy vibes from the dialogue.
On anachronism:
The qualities I admire in the character of Indiana Jones, and which make him a hero to me, are courage, intellect and quick-wittedness, an absolute inability to quit and a respect for the past. These qualities are timeless and their use in a colonial system is not necessarily or automatically an endorsement of colonism.. And, not for nothing, some of these qualities you readily admit you admire in the Hovitos of the film. But the Hovitos of the film were trying to kill Jones upon the instigation of Belloq. If rooting for Jones is implicit approval of colonialism as you imply, then rooting for the Hovitos of the film is implicit approval--not for the Hovitos culture--but for the instigation from, and even of Belloq himself. Do you see?
I consider it unfair to judge those who've gone before by the standards of those who are going now. (What will the people in 2086, for example, say about us in 2021 that we don't even consider now?) I grew up reading my grandfathers rare first editions of Tom Swift adventures and Edgar Rice Burroughs' Tarzan books. While they certainly contained aspects of their times that would be objectionable if written today, I never felt propagandized towards those aspects and remember strongly and mostly the primary celebration of intellect and courage and adventure.
The real villains in Raiders are generally cowards (they rarely fight one-on-one, instead throwing their henchman between them and violence), are generally stupid and self-centered and have no respect for the past. And, because they are this way, they get their come-uppance in the end. That, too, is one of the things that make it a great movie.
