Yes, I did pick up on that same dichotomy. I think somehow Brenda's sister interprets things differently than I do, which of course is what art is about, and she does reference things that are not likely going to be in the series (like the second trial). I don't think the series depicts Brenda as involved with the "school of the prophets" her in-laws are becoming increasingly invested in, I think just the opposite. And, I think Brenda's opposition to them, and support of other family members who are concerned and lack of support for her husband, are directly related to why she was murdered. Brenda's sister (Weeks) seems to believe it was much more about the group's political ideation. The authors (both of the book and the screenplay) are trying to make a point, and like it or not it's a relevant point - some of those off-shoot groups have their faults which can be dangerous (and the church has been deceptive in the past). In the end, Brenda and her young daughter were murdered by leaders of this group who also happened to be family members, regardless of whether it was about polygamy, fundamentalism, anti-government, or anything else.
I think episode 4 dragged a bit and perhaps the story is being stretched out too much at this point. That's just my opinion, and it's not like there wasn't anything that moved the story forward. But with only two episodes left it seems like they may now have to cram some stuff in. (Although I don't know at what point the story ends in this series - does it end with arrest or trial?)