Would we really be making such a fuss about Narnia if it was one of the male characters who had become interested in lipstick nylons and party invitations... Erm... Actually, we probably would come to think of it...
You can look at this issue in any way you want and draw whatever conclusions you wish and the stories themselves don't change an awful lot over all. Weather or not you enjoy them is another matter entirely. The question 'did you understand it?' does not always equal 'did you enjoy it?' I didn't, and still don't fully, understand The Last Battle, but found it an interesting read and did actually like it.
I think nowadays it is becoming increasingly difficult to make a fantasy without having such interpretations and themes planted on it, some of which the writer may never have had in mind. I think Lewis said something along these lines in something or other. Narnia comes into a lot of criticism for the villains wearing turbans and how that makes it all racist. But I'm not sure. It may be a case of needing a villain and the seeds in the past (namely in The Horse and his Boy) have suggested one such people who could be called upon to play the roll. But I'm no mind reader and cannot say for sure and would probably have to give Narnia a proper reread at some point to give a full account.
In terms of Pullman he set out to have his villains as representing a certain group, namely the religious establishement. I think this is where he comes into his criticism. By saying it outright he loses the subtlety that he could have had by leaving it ambiguous and open to interpretation. But then again, he probably didn't want it to be open to interpretation.
I think this is why we are still talking about Tolkien. He rarely, if ever, gives concrete 'this = that' analogies for anything. There are sometimes rough outlines, (his comment on what the function of each race was in a BBC interview springs to mind) but he says this in a glib fashion that suggests 'well it could be anything.' And so it can run away with you. Pullman obviously wants his message to dominate the reader's attention. This is by no means a bad thing if you agree with him or not. Beginning the book with the 'This person is wrong and everything he says is a lie' stance is not going to give you an enjoyable read in most cases.
Yes I am comfortable on this fence.