This fascinating article in the New Yorker is built around the stories of ex-Scientologist Paul Haggis. The article seems remarkably fair-minded and careful and Haggis himself seems remarkably sensible.
I do worry about the government poking around investigating organizations that, whatever they may be for those who run them, are genuine religious organizations for most of their members. It is so very easy for the powerful to go after people who are different, whether because of their sexual behavior, their politics or their religious views. Defending people who are different is in some sense integral to defending freedom itself. I would much prefer to see bad behavior around religious organizations brought down by information, as in the New Yorker piece, than by the state itself.