-I was under the impression that Monneypenny was temporarily re-assigned to administrative duties while a review was conducted in the wake of what was essentially a failed mission. She discovered a liking for administrative duties and therefore stuck to that instead. There is nothing sexist here. It's quite common in many Bond films for Bond himself to be suspended of his duties following a failure, although he usually goes ahead and acts on his own anyway. And there is nothing sexist about choosing work you prefer doing.
When arguing whether a film is sexist, i.e. a product of cultural patriarchy, I don't think one can argue like this, as in within the context of the plot and character machinations as portrayed in the film. You have to argue outside of that, and whether the film needed to be written like that in the first place.
Just for argument's sake...
of course a sexist, chauvinist, patriarchal writer is going to
write Moneypenny as a woman who
likes clerical duties. You even provide an example...of course Bond always does what he wants, avoiding desk duty, and being a man of action, while the woman decides she likes clerical duties. Writing the character wanting it doesn't mean the film isn't sexist, it just means the writer is trying not to write it that way.
I really don't believe the Moneypenny situation is an inherently sexist one, I believe they're just trying to set up a classic Bond trope for future films. But in the discussion on whether it is sexist or not, I think one has to argue in the context of the creation of the film, not what takes place fictionally within it.