I think that this is actually the point of the text. The author clearly wishes to retell a patriarchal legend from a female perspective to give a more rounded and realistic picture of a legend that seems to consign women to play the part of stereotypical figures. Morgana le Fey is traditionally thought of as nothing more than a two-dimensional witch who opposes her half-brother's rule and is an evil character. Bradley seeks to reclaim her character, telling the story from her angle, and producing a fascinating novel as a result. Note the following quote that comes towards the beginning of the novel:
There is no such thing as a true tale. Truth has many faces and the truth is like to the old road to Avalon; it depends on your own will, and your own thoughts, whither the road will take you.
In a sense, the novel is clear that it is not offering an alternative truth, it is merely trying to develop the reader's perspective and help them to see that there is "no such thing as a true tale" by rewriting the Arthurian Legends from the position of Morgana. However, our interpretation of this perspective as readers is based on our will, thoughts and where the "road" of our imagination takes us. Bradley therefore did not go too far in offering a feminist view of the Arthurian Legends; she did so only to enlarge our appreciation and understanding of the original tales and to flesh out certain undeveloped aspects.
I don't see this as a femenist book at all, the story is told through Morgan Le Fey's eyes so naturally she's not going to conform with the generally accepted male ideas of the era. Honestly I thought if there was a theme Bradley was going for other than flipping the Authorian Legends of its head, I thought it was more about the intolerance of religions in past and present. The only reason this may look like a femenist book is because Bradley portrays pretty much every single religious figure as an embicile who were all men and the only powerful people in the book are men (it wouldn't make much sense if they weren;t considering the period.)
Try not to see this as a girl power book and re-read it with the idea of religion in mind and the time period of King Arthur rather than sex. It wouldn't be as strong of a book if say Lancelot or had taken over Camelot because in reality any man could have feasably taken over Camelot. Bradley instead put a woman in charge because that was the least likely thing that could have possibly happen in that time period.