There are legends that also have Morgana as the lover as well as student of Merlin. We don't have enough yet to make a call unless we've missed some clues, which is certainly possible.
It's hard to know what would influence Jim more - the older tales or the newer adaptations. He's often said he's more partial to the newer stuff yet he just as often picks more obscure legends and older tales (like Ethniu) which makes me think it could be some intentional misdirection on his part.
I don't think we will know until the BAT sadly.