The 2008 worldwide protests of Scientology is the biggest part of Scientology's downfall. The closest the show has come to recognizing this is having Mark Bunker & Tony Ortega on for an interview. But seriously, I'm not demanding they put on the Guy Fawkes mask and salute. But considering the US (and some public opinion) still considers Anonymous a terrorist group; They should validate what Anonymous did.
Season's over. They're probably going to do another one, but it's a little late now.
There's still a lot more to cover, but I'm pretty sure the whole point of the show was to talk to people who were Scientologists and see what it was like during and after. Most of them pretty high up in the CoS.
They didn't even talk about Tom Cruise or John Travolta outside of a few mentions here and there and they're the posterboys for Scientology even more than David Miscavige.
I think the show is about informing people in the outside world about what Scientology is like, and we already knew about the Anonymous protests.
I'm sure they'll get to in in Season 2.