The Myths and Legends of the Doctor have always been distorted. There's no reason why the Doctor can't be Merlin, without having actually participated in enabling the seedier things, such as the "rape".This has been mentioned before, but we know from Battlefield that at least one future incarnation of the Doctor will become known as Merlin in a parallel continuum. But there's one thing about this scenario that doesn't sit well with me: In the Arthurian myths, it's Merlin who disguises Uther, Arthur's father, as Igraine's husband, the Duke of Cornwall, so Uther can sleep with Igraine and sire Arthur. Would the Doctor really aid a man in exercising his lust, helping him deceive a married woman into having sex with him? I have difficulty seeing the Doctor willingly engineering such a scenario, which has its roots in violence and petty lust.
The Doctor may have simply been involved in something, totally unrelated, that eventually led to Uther being able to use the disguise