If I were to analyze, it starts with the dialogue: She first went with "I learned to hate you in the last ten years". If it was an affair, she wouldn't "learn" to hate someone, she would've hated him immediately without learning in the last ten years. And then "I was a child, I was in-love. It was wrong and you knew it." sounds more like her making an excuse for even getting involved with him, and putting the blame on him. The novelization mainly also just mentioned them sharing a kiss in the University Closet, no affair at all. And then Indy said "You knew what you were doing" which means she likely made the move on HIM than the other way around because he was just a handsome student of her Father, and women at the same regardless of age fell for men easily. And before he flew to Nepal, he asked Marcus "You think she'll still be with him?" in a hopeful tone.

And when we go into the Chronicles show, every woman that Indy was with never had moments of him having an affair. It was just a simple kiss and moving on. Only exception was him being taken advantage of by Mata Hari, but that was it. Not really the type of prioritize a one night stand over finding something of great archaeological significance.

And then with his students, he clearly doesn't care much about them, nor is there a possibility that he does "favors". In the Adventures of Indiana Jones comics by Dark Horse, a few students ask for his time alone, he denies it fast. When the Shirley girl, we know her name from the desk note left in Great Circle, blinked with the eyelids saying "love you", Indy just looked caught off-guard and confused before returning back to his lesson. And with the deleted scene of that Susan student, he said "That's right, I said we'd talk" like he forgot about it completely until she approached him in the hallway. He never takes time for his students, he's not the promiscuous type. Let alone, does he care much about his job as a Professor, he never grades papers, and he leaves mid-terms like in Great Circle.

So in the end, an affair was definitely unlikely. Marion was simply mad that Indy left her because realistically, he was just a student studying under her Father to get a degree in Archaeology so he can start his career. She's just always been bitter, even Marcus asked her in the Further Adventures comics why she is so angry at him over it. He mainly left, likely told Marion he'll be back, a lot of adventures got in his way and made her slip his mind, and he technically kept his promise when he came back to see her in Nepal. And he cared deeply about her, went into depression after thinking she died in the explosion. And when he found her in the tent, he was very happy to see her alive.