I don't think the disgust for this story is overblown, even slightly. In fact, I think it doesn't get brought up enough.
No, it wouldn't have been any better if the Supreme Intelligence was behind it. That's like asking whether it's better to be beaten to death with a hammer or a pipe. Either way, I'm still being beaten to death. The rape, itself, and the reactions of the team were what made the story so disgusting. It was horrible enough to put Carol through this, but on top of that, her team (her friends) acted completely, idiotically bizarre. To this day, I don't know how Carol sits with these people. I don't know how she trusts a single one of them to have her back in battle again.
Don't think it was retconned... but everything about Kang confuses me.
She drank a lot and forgot it. Actually, in modern comics has this ever actually taken place, or has it been retconned?