Since I have some spare change rattling in my pocket... I haven’t played the Imoen Romance, so I’m talking on a general level here.
In the real world, the nice people in white coats mainly set the rules for the children of the gods. Barring that, what kind of moral code is there – in the real world, or in FR? I don’t think that demigods, or their relationships, are quite commonplace in Faerun, either, even though they do exist.
Everyone, myself included, may have his or her own opinion on the matter. If we have trouble deciding on what’s allowed and what isn’t, why would the characters themselves find it any easier? Why not make the points that have been made in this discussion in-game? By now, it should be safe to say that different protagonists, played by different people, could have different reactions to his/her heritage, as well as Imoen's. Suppose, for instance, that Charname has had this soft spot for Imoen for some time now. He finds out she's a Child of Bhaal as well, feels queasy because of the implications, tries to figure it out, and finally decides she's off limits. That's one simple possibility, and there are others besides "torrid incestuous affair" and "uncomplicated, siblingly and platonic coexistence". And, as has been stressed before, "character" is the operative word here.