Of course it's an allegory.
Every fantasy story Donaldson writes is an allegory. To Donaldson, fantasy is just the externalization of internal conflict.
That said, it's also just the externalization of the internal conflicts of the the
characters. Like Linden. Linden in real life is struggling with this idea that only she can do anything effective and having to protect Joan from a crazy man, Roger, who nonetheless is connected somewhat emotionally to her through his father. Hence, the effective type folk are Giant women, the crazy giant is male, and the truly tortured is a woman because that what Joan is, who Linden was focused on before hand.
All this is just within the text. I don't have to speculate on Donaldson's upbringing, education, and so forth just yet to get this meaning.
That being said, once this happens, we can take author experience to see why he does what he does. For example, I see a few similarities in style with Ford Maddox Ford. However, this doesn't help me interpret what the story is about.
Ultimately, I like to approach the meaning in reference to the text first. With some authors, this isn't enough and you have to actually know more about him and his time to properly understand the work (Like Dante's Divine Comedy). And sometimes, an author will purposefully throw in external references as a cue for the reader to consider outside sources (Like C. S. Lewis' Chronicles of Narnia or T. S. Elliot's The Waste Land).
I guess what bothers me is not the technique of considering the author for understanding the story, it's that I feel you haven't considered what can actually be gleaned from the text first before turning to external sources. Like Joan was a traitorous bitch waaay before the Last Chronicles (and before Donaldson went through a divorce... let's not beat around the bush here). But just this combination of internal and external evidence can show that there is something else going on than a study on gender condition.
Paradoxically, the idea that Donaldson writes fantasy as an externalization of internal conflict is from an outside source, but there's hope in contradiction
