For what it's worth, I don't see any point where Lucas suggests that Indy actually
had sex with the teenaged Marion, simply that they "had an affair." That could mean an emotional affair or "affair of the heart," i.e. a chaste romance. Heck,
Wikipedia says that even today, extramarital affairs are more often emotional than sexual. And we are talking about the 1920s here, which, though one of the most sexually liberated decades of the early 20th century, was probably more chaste than modern times.