When I saw Raiders, shortly after it was released, I didn't view Jones as anything but a character in context. Of course he raided sacred tombs to steal treasures, regardless of any religious significance they. might have to the their indigenous creators.
And, of course, such behavior would not be countenanced today.
Is Lara Croft a hero, or villain? Didn't she also slaughter an impressive array of endangered species, at least in the initial versions of the game, in her quest to steal ?
I think the problem with Jones as a character is that he was written in homage to the 30s & 40s movie serials that Lucas, Spielberg & Co didn't quite grow up on (both were born in the mid-forties, American Grafitti reflected their cultural mileu more accurately; Raiders was their parents' upbringing). Jones's activities, his privilege, etc all were pretty much taken for granted.
I don't think anyone expected Raiders to become the smash hit & Jones's character to become a franchise the way it did. Edgy characters are often softened, made more palatable, as they proceed. Witness Harris's treatment of Hannibal Lector. He is transformed from a minor, but still significant character in Red Dragon, to something resembling a Nietszchean Overman in subsequent books. He "prefers to eat the rude" i.e. characters we don't like. Some of his colleagues even suggest he transcends the human, which from a moral standpoint lets him off the hook entirely.
In short, very different from the imprisoned killer Will Graham visits in Dragon.
I think the same is true for Jones. Hence he does a good deed in the first sequel, which was otherwise a ridiculously bad film. (The other two were only moderately bad).
Now, Marion? No. Not buying the underage thing. First because I thought Karen Allen portrayed a woman older than her actual age. Second, because unless I'm totally blind, there's no hint of older-younger, or under-age fetishization in any of Lucas's other films. You could argue that both lovers are infantilized by their hairless in THX 1138, but that's about it.
One final point, I think people forget the degree to which, in the 1970s & early 80s, age of consent laws & mores were regarded as regressive & patriarchal. I think people then would be shocked to learn that the age of consent is 18 (across the US, I believe) & that a 19 year old having sex with a 17 year old would be liable for rape charges.
That's not to to excuse anything—I don't think Lucas seriously meant for Jones to be having sex with a 12 or even 15 year old Marion—but rather put it into context.