I think it might actually be thousands of years before the Dune films. The Dune universe is on a very long time line and yes, the Bene Gesserit have a very, very long time line for their plans and they have a very specific goal that I will not spoil.
Lady Jessica was still a Bene Gesserit Sister, but they were not happy with her because she was supposed to give birth to a female Atreides child that would be married to a Harkonen male, likely Fade, to move forward the Bene Gesserit plan to eventually produce the Kwisatz Haderach. Instead Jessica gave birth to a son, Paul, because Leto wanted a son and Jessica fell in love with Leto. The major issue the Bene Gesserit had was Paul was not under control of the Bene Gesserit and not who they expected to be the Kwisatz Haderach (and maybe he really isn't, but that's a whole other story).
By the way, Jessica was not married to Leto, she was his sworn concubine which was a deal arranged by the Bene Gesserit. It's just that she was supposed to have Leto's daughter, not his son.
By the way, this complexity in back story and relations is why it is so difficult to make the Dune movies. There is so much background untold and, while I loved the new movies, they left out quite a bit or at least didn't bring it to the forefront. Specifically things like the nature of religion, the nature of power, environmentalism, the dangers of A.I., etc. Though the religious stuff comes more into play in Dune: Messiah.