The planetary governor in the Crimson Fists novel is female. The Ordo Malleus Inquisitor in the first Grey Knights novel is female. You can buy female inquisitor models as well as the SoB range. Of course, the SoB look like dominatrixes but I'm not sure that counts as misogyny unless the bulging muscles of the Catachan models also somehow represents a diminutive broadside at males and/or you've spent the last twenty years reading Katherine MacKinnon and Andrea Dworkin.

Being a generally left-leaning liberal type I can think of lots that is 'wrong' (IMO, of course) with the fascistic, totalitarian politics of the Imperium... Misogyny isn't one of them though.