It has been speculated that the producers (Tom Hanks and others) are not happy with the Mormons. The Mormon church was a vocal proponent of Proposition 8 (eliminating same sex marriage) in California...a proposition that Hanks and many others fought against. There is a some controversy in how the Mormon church used their pulpits to encourage their flocks to vote yes and to donate money in the effort to push it through.
The show, in its first season, started out fairly innocent...how a fundie LDS who believes in "The Principle" of plural marriage survives in a society that condemns his beliefs. They introduced the Juniper Creek compound and explored the cult environment of this off-shoot sect of the main LDS. The first couple of seasons though, they never really brought the main Mormon church into any of the story lines. This was strictly about the off-shoot polygamist beliefs.
This season though, they've pulled "The Church" into it hot and heavy...up to the point of the church's attempt at trying to squelch information that the church never meant for plural marriage to go away from their official doctrine. Now, they're going to "expose" some of the "secret" rituals in an upcoming episode.
Could some of this exposure of the church's "secret" rituals be in response to their Prop 8 actions?