“Are you saying that a mechitza is not halachically required in a shul?”
No.
“Or are you saying that it used to not be but now is?”
Not necessarily. I am saying that the requirement for a mechitzah is almost certainly a d’rabbanan (at most), as (1) the mitzvot for which mechitzot are required are d’rabbanans, (2) there was no mechitzah in the Beit HaMikdash except for Yom Tov, (3) and even that balcony was only instituted by rabbinic decree at the very end of the Bayit Sheni period, (4) were such a balcony a d’oraita the people who built Bayit Rishon and Bayit Sheni would have been over a d’oraita, chas v’shalom, which is impossible, (5) even after the balcony was built, a woman could still enter the priests’ courtyard itself to shecht her own korban with the male priest right next to her capturing the blood, (6) not only does the gemara in Chullin say that a woman can shecht, but (7) the mishnah in Middot says that there was a separate women’s entrance to the priests’ courtyard. This is all documented in rabbinic sources. Rav Soloveitchik z’tz’l held that the requirement for a mechitzah is d’rabbanan.
However, it is possible that mechitzot were ALWAYS required in a beit knesset as (1) a beit knesset is very different from the beit hamikdash, (2) we don’t know exactly when the first beit knesset was built, (3) at the very institution of communal tefillah the Anshe Knesset HaGadol might have included a requirement for separate seating and a mechitzah. However, with the exception of the attribution of the institution of tefillah to the Avot, and to the Anshe Knesset HaGadol, there really aren’t any sources to back this up that I have ever seen. I heard from Prof. Lawrence Schiffman that the very earliest written documentation of a beit knesset (during late Bayit Sheni times) is actually from a Christian source. We have lost so many of our sources :(.