Is there a Halachically permissible way to bring the Torah into the women’s section after Kriyah (thereby not returning it to the aron in the most direct rout)? if not, is it permissible to wait in the front or back of the women’s section and have them walk to it. Assuming it is in general not ok, If a shull currently has the practice of bringing it in, would that provide basis for a leniency?

There are many Halachik issues which are not just decided by the "technical" aspect of Halacha, but also by "Minhag"= custom. The way things are conducted in a Shul are also governed by Minhag. The order of things in Shul and are not supposed to be changed. See Responsa of the Rashba vol I., 323, and Responsa of Rav Kook zt"l, Orach Mishpat 35. Rav Moshe Feinstein zt"l forbade new Minhagim even which are theoretically permitted if the motive for the new practice stemmed from the dissatisfaction of existing ones. (See Igrot Moshe Orach Chaim Vol. IV, 49) Furthermore, new Minhagim are meant to be instituted by Gedolei Yisrael See Magen Avraham on the Shulchan Aruch Orach Chaim 690: 22. So until Gedolei Yisrael institute such a practice, I would refrain from doing so.