the apparent exception was readily seen to be charmingly and ineffectually disguising her true womanhood

In Victorian times, attitudes to British women were oppressively and distortingly stereotypical:

During the reign of Queen Victoria, a woman's place was in the home, as domesticity and motherhood were considered by society at large to be a sufficient emotional fulfilment for females. These constructs kept women far away from the public sphere in most ways

bbc history

To maintain such attitudes in the face of the reality that some women could write, paint, be scientists, organise, run businesses and all other activities of intellectual competence, some men (and indeed, some women) erected fallacious conceptual frameworks of belief that reinforced the domestic stereotype by only acknowledging these other abilities as mere decoration on the central and definitive fixed idea of domestic womanhood. Thus Lewes, while admitting to the genius of a woman in respect of literature, sidelines it as a merely delightful diversion and unsuccessful cover for her true nature (as already immutably defined by Lewes). Essentially, these foolish men defined a woman of ability or genius in their own stereotypical terms and then dismissed any evidence to the contrary by placing it in a separate part of their minds.

I think the key words are "charmingly" and "ineffectually." This suggests a very patronizing attitude toward women of genius: that is to say, perhaps, how adorable it is that these women are trying to behave like men. That's how I would interpret it, anyway.