Character reason aside, I saw on the bonus DVD that they were going to use Marion again, but decided to give Indy a new girl in each film. To make it easier without having to explain what happened to Marion, it would be easier to make it a prequel. Audiences would not expect an explanation if the movie took place before the events of Raiders. They also wouldn't expect to know what happened to Willie because Raiders takes place after, but was filmed before. I hope am I making sense.
Now, since LC was filmed a few years later, and they had the original James Bond, a man who was the epitome of "love 'em and leave 'em," they probably didn't care enough to explain what happened to Marion. They probably thought that not explaining what happened to female leads hadn't been a problem for Bond films, it probably wouldn't matter much in this franchise either.