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As we discuss here, there are differing views regarding whether a women's section in a synagogue has the same level of sanctity as the men's section. Even for those who maintain that it does not, their concerns would seem to be specific to a synagogue: that the minyan (and perhaps the aron kodesh, etc,) is centered in the men's section as opposed to the women's section.
The Talmud (Megilla 27a) teaches that a beit kenesset can be turned into a beit midrash. Rambam (Hilchot Tefilla 11:14) explains that this is because the sanctity of a beit midrash is considered to be greater. The source of its high level of sanctity is the Torah learning that takes place within it (Sefer Ha-batim, Beit Ha-mikdash U-veit Ha-kenesset 10:12). The respect due to the Torah that a beit midrash represents also incurs sanctity (Rambam, Sefer Ha-mitzvot, Prohibitions, 65). A distinction can be drawn between the sanctity of a beit midrash for the public and one established by an individual only for personal use (Shulchan Aruch 151:2), so that benefit to the public is also a factor in a beit midrash's sanctity.
A women's beit midrash typically serves a public, and not just an individual, and the learning that takes place within it is recognized halachically as Torah learning. (See our discussion here on women's recitation of Birchot Ha-Torah.)
Since the beit midrash's sanctity is rooted in the Torah learning that takes place within it, and not in minyan or the presence of an aron kodesh, it follows that a women's beit midrash has a full measure of sanctity.
One caveat--it is common for batei midrash and batei kenesset to be established conditionally, to allow for relaxing some of the strictures about behavior within them. (See Shulchan Aruch and Commentaries, OC 151:11.) Those laws, too, should operate similarly for a women's and men's beit midrash.
The Talmud (Mo'ed Katan 18a) assumes that women are not often found in the beit midrash. What a beracha to live at a time when women's batei midrash have proliferated to the extent that questions like this arise!
See more Q&A here.