There are many Celtic traditions evident here, not just of fairy queens ruling magic lands, but of actual sisterhoods of healers and miracle workers recorded in classical literature. Such a group might have been led by a priestess that served as the earthly manifestation of a goddess. Giraldus Cambrensis and other medieval authors were well aware of Morgan's divinity. Comparison of Welsh and non-Welsh Arthurian matter show her to be somewhat identified with Modron and ultimately with the river goddess Matrona, similar to and possibly derived from the Irish goddess Morrigan.
Christianity humanizes and eventually vilifies her. Early on she is a type of benevolent fairy that aids Arthur throughout his life, not just at the end. The Welsh claim her father to be the obscure Avallach, king of the magical island with it's Welsh name, but he fades from legend. Morgan is essentially the sole personage of Avalon, the Isle of Apples. She is further humanized with the progress of Arthurian storytelling. The former goddess becomes a daughter of Ygerna and her first husband Gorlois, the Duke of Cornwall, making Morgan Arthur's half sister. Glastonbury's identification with Avalon leads to beliefs that she ruled in that area but romances place her in various locations. She becomes the owner of the Castle of Maidens, possibly near Edinburgh while a few continental romancers move her to the Mediterranean entirely. Sicliy is one such place. She is named Fata Morgana by the Italians and that name is given to a mirage that appears in the Straits of Messina attributed to her magic in the past.
Medieval Christianity had a difficult time assimilating a benevolent enchantress, she becomes more and more sinister. She is now a witch taught the black arts by Merlin and is a bedevilment to Arthur and his knights with a special hatred towards Queen Guinevere. Oft times she is involved in a plan to ensnare a knight for her own pleasure by sending them into a "valley of no return," or against a mighty adversary. Other times she is married to Urien and bears a son, Owain or Yvain. Yet she never becomes purely evil. Many attractive qualities remain and Morgan is associated with art and culture. Despite the scheming and plotting at court, she is still the one who bears the wounded King to his place of healing on Avalon.
Part of Christianity's failure to understand the character of Morgan was their misapplied versions of morality. They imposed a Judeo-Christian ethical structure over a Celtic one and tried to eradicate the conflicts. The monks basically misunderstood the beliefs of Celtic rule. Women had equal if not greater power than men and were expected to take lovers. This is evident in the transcription of the Tain, the national epic of Ireland (except here scribal ignorance of Celtic ways actually preserved many of them). This is also the reason why Guinevere is seen as unfaithful rather than a free woman free to make her own choices in who she beds. Morgan necessarily becomes a witch to explain her sexuality.