It's possible that Lucas actually thought that Indy and Marion were now a couple and he wanted to make a movie which had Indy unattached. Either they break up or Indy is not allowed to be romantically involved with a character like Willie.
It's something that cropped up in previous pulp fiction. Edgar Rice Burroughs married Tarzan off in his second Tarzan novel. He managed the next novel by separating Tarzan from Jane and then (4th novel) they had a kid and Burroughs immediately had the kid grow up and paired him off in the same book. Later in the series Jane was often simply forgotten (sometimes literally - Tarzan was prone to amnesia). Prince Valiant almost shuddered to a halt when Hal Foster couldn't keep his hero unattached...
He might also have liked the idea of stepping back, at least by a year, from WWII. In any event, many people didn't even notice that Temple of Doom was a prequel.
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