it just seems unexpected, if AF was indeed such a strong catholic...

Well, I think she was capable of writing against her own convictions to make a sympathetic character express a view that she herself may not have held. I've actually no idea where she stood on homosexuality: I'm not sure, anyway, that Christianity of any denomination has always been quite so obsessed with homosexuality as it seems at the moment. I think it intersects interestingly with social class, as well: the sprezzatura that is is presented as so admirable in the Marlow books would, I imagine, be rather snooty about over-regulation of sexual mores.