Most people don't think about Scientology being an religion or really care, in my experience. They think of South Park, Tom Cruise, and whatever the Tampa Bay Times has published about them (at least in Florida). As far as the general public is concerned, I don't see how arguing that particular point is going to turn anyone's opinions around.
I understand why it's important here and to scholars of religion.
Louis Theroux calling it a religion is not going to help the CoS turn opinion around.
It's cumulative. Most people repeat what they hear others repeating. The reason Miscavige instructs Scientologists to say "religion," etc., practically every other word when mentioning Scientology, is that the "Scientology-is-a-religious-organization" meme has not been adequately embedded in the public mind.
Once it is embedded, expect to see a sea change: a shift. The "hater" and "bigot" card will be played with more frequency. Slowly, the "general public" (and also the media) will become timid to criticize the "religion" of Scientology.
This is the plan, and it's not unrealistic, in this age of inhibited speech, political correctness and hate speech laws, that it will happen.
The question is how much do we want to assist Scientology in this endeavor?