Obviously, it's true that much of what makes us uncomfortable about Scientology is unique to Scientology. I think I was pretty clear about Scientology's unique oddness, its propensity for authoritarianism, etc. In fact, I linked to the exhaustive Rolling Stone piece that is if anything far more damning of Scientology than the Time piece you linked to (and I said I find it generally persuasive). So obviously I was making a circumscribed point, one which I think holds: Scientology is weird, but so too is religion weird, and we shouldn't sit there in Mass or Shabbat services and be so smug.
I do think Scientology has ruined lives. I think many, perhaps most of the horror stories, that we read are true. But if Scientology has 8 or 10 million members -- and I think that's a big exaggeration they make, so let's say 1 million committed members -- than even several hundred of these stories, however lurid and true, wouldn't make Scientology worse (by our admittedly fictional, utilitarian/consequentialist calculus) than other faiths. I know people whose lives were destroyed by Opus Dei -- indeed, I know people whose lives were destroyed by the massive church coverup of pederasty. I know people destroyed by the evangelical subculture, by the mainstream Mormon culture, by Judaism.
Here's the higher-order point: we shouldn't think about religions in terms of their worst excesses (take that, Mr. Hitchens).
We might, however, ask if there is something/systemically/ corrupt about certain religions. That's the implicit charge against Scientology: that something in its nature makes it inherently cult-like or authoritarian (more so than, say, Catholicism or Islam or Orthodox Judaism, all of which can be quite authoritarian in their ways). And I just don't think, based on my reporting, that the answer is obviously “yes.” I think power corrupts, so the leaders are going to be more corrupt than the laity. I think zealotry is bad, so you'll find more excesses among the “Sea Org” than among the more everyday Scientologists. But the point is that there /are/everyday Scientologists -- I've met dozens of them -- who aren't rejecting their families, aren't turning over all their money (or even much of it) to the Church. The point is that one can be a casual, or occasional, Scientologist. And that's what gets lost in most of the reporting on the subject.
I take the last point, but it doesn’t seem to me that the existence of “casual, or occasional” Scientologists exonerates the Church from the charge that it’s more inherently dangerous than, say, Lutheranism. (Full disclosure: I have a relative who is a Scientologist; we’re not terribly close, but so far as I can tell he fits the “everyday Scientologist” category that Oppenheimer identifies – he hasn’t rejected his family, turned over all his money, etc. etc.) Nor do I think that most people find Scientology suspicious primarily because its beliefs seem wackier than the doctrines of many mainstream faiths. Yes, people mock the weird teachings – the aliens, the volcano, the intergalactic civilizations, and so forth – that L. Ron Hubbard's Church allegedly reveals to its initiates. But what's most troubling about Scientology is precisely what Oppenheimer identifies as the crux of the matter: Namely, that it seems deliberately designed to be "cult-like or authoritarian," and that the horror stories he mentions, which range from brainwashing to fraud to worse, may represent not an excess but a fulfillment of what Hubbard had in mind when he founded the religion in the first place.
Obviously, every faith that lasts long enough produces institutional abuses (and worse); the question is whether one can have the religion without the abuses, and the more that the answer seems to be no, the more it seems reasonable to treat that faith as inherently rather than incidentally dangerous. This is why there’s so much debate about whether Mohammed was teaching bin Laden-style jihad right from the beginning, since the answer goes to the heart of how we think about Islam today. Or again, if there were evidence that Jesus of Nazareth had intended to found a religion dedicated to enabling and covering up the sexual abuse of children, then the Catholic sex abuse scandals would be cast in a very different light.
And in the case of L. Ron Hubbard's cash cow of a Church, I've read and heard and seen enough to give me a strong sense that the inherently-dangerous side has the better of the argument, and that a Scientology purged of its "worst excesses" wouldn't be Scientology at all.