This is part 2 of an extremely long post; part 1 is here.
I'm not going to beat around the bush; I had fully expected some sort of attack on religion, or at the very least on groupthink. But Minear was more clever than that, and it seems that Whedon is as well. Instead of simply doing a "cults equal badness and so does religion" thing, Minear explored how others would (and could) manipulate religion as they would manipulate anything else. As Minear said in an interview,
...I wanted the story turns to be rooted in the Dollhouse premise so I used the sci-fi angle to make a scientific miracle.
They could create a real woman who had really experienced a divine vision. And the fact that she was really blind proved that she wasn't lying. That's why she could recognize Sparrow through touch because the vision she experienced was no lie. Granted, Topher put it in her head, and we saw the 3-D model of Sparrow's head and understood how this was accomplished, but to Echo/Esther, all was true. So when Sparrow knocked the cameras loose and her vision was restored, this was also really a miracle... to her.
What was so amazing about the episode was that it wasn't a falsely religious man using religion to control the masses. It was the outside world, the - ostensibly - good guys who used religion to manipulate, to control. It was the ATF and the Dollhouse who created a situation where a cultish religious leader could come to depend on miracles, where such a man could be convinced that he had been featured in a vision and had been witness to a restoration of sight. These were true believers, even Jonas Sparrow. Unlike Scott Tobias of the A.V. Club, who said, "the fundamental problem for me is this: Sparrow knows he's not a prophet. He knows he's every bit the Mitchum-like charlatan. So when Esther talks of visions and recognizing his face from a dream, that should be proof enough that she's an imposter", it seems clear to me that Sparrow really does think he's doing the best for his community. He's not a Jim Jones type; this much is clear from the fact that his flock is both shocked at the fact there is a cache of guns underneath their feet and by the fact that he does believe Esther. He doesn't make his group take up arms. He isn't interested in pulling a Waco and holding a shoot out. He believes, truly and deeply, that there is another way and that God will deliver him and his people. That he is a true believer doesn't make him any less dangerous; he's still willing to condemn his people and himself to death. But it does offer a more nuanced layer to an episode that could have just been a retread of old ground. Whedon and Minear manage to make the cult seem like something other than an egotist's creation for his own validation.
At the same time, even though it is not a condemnation of religion or even this religious expression, there is an exploration of this idea of purity; of being able to get back to the garden, or to recreate the garden. Such a sentiment has been around for eons, probably since the first tale of lost paradise entered the conscious lexicon. Even Joni Mitchell declares, "We've got to get ourselves back to the garden". Whedon has tackled, though only briefly, this subject before; in one of the coolest feminist moves, Whedon discarded the idea of our world beginning with a lost paradise on Buffy the Vampire Slayer, and instead declared that it had been a hell - that the books were wrong. In Serenity, we saw the Operative working toward creating "a world without sin". But the only world without sin we are shown is a dead world. Here, the world without sin is the pinnacle of achievement in two places, the Children of the Temple's compound and Adelle DeWitt's Dollhouse. As DeWitt says at the end, "A place of safety, of untroubled certainty, of purity. This is the world we must maintain. It is imperative that nothing disturb the innocence of life here. Once any temptation is introduced, it will spread... like a cancer, and all will be infected." And yet, Victor's reaction to Sierra is, in its own way, pure and innocent. His attraction to her is a normal, natural part of life, and only when we consider human sexuality something that creates a less than pure being does Victor's "man reaction" cause concern.
What seems clear is that even scrubbed, even erased of any and everything that makes us what we are and what helps shape us, some bit of us remains. There cannot truly be a world without sin, and what's more, we probably should not even want it. The Actives in the Dollhouse come the closest to being without sin, and yet they aren't something I would aspire to be. The world is messy; but it is conflict that helps shape us, and there are things considered 'sinful' - mostly in connection to sexuality - that are a necessary component of life. To bind a sin to something necessary to the very proliferation of a species seems particularly sadistic.
Note: There may be one more post coming; I still have thoughts, but it doesn't really fit with the religious flow of this installment.