unfortunately with the nature of scientology, hiding identity is needed.
Oh, for Anonymous themselves, most definitely, but for some chump holding a sign outside a CoS? Not at all. People have been doing that without masks for at least a decade, and they've gotten away with it. The thousands of people on facebook and flickr who have directly linked their names with anti-Scientology groups have also been perfectly fine. Lets not buy into it all and be overly melodramatic here, the chances of any sort of retribution for participating in a protest like this are slim to none unless you currently or previously were employed by the CoS (or signed any sort of contractual agreement you would break by speaking out).
As far as discrediting goes, Scientology's "official policy" on this more or less refers to professionals, journalists, former members, and public figures (or, at least historically, that's where the evidence lies). The actual documented methods of them doing this rely on legal action and borderline harassment through the legal system, general professional censuring and discrediting. How are they going to discredit any of these protesters "Uh, he makes shitty 6" pizza subs? She's always late for her shift at TGIF? That guy got fired from Burger King?" The protesters do themselves a disservice here by wearing the masks. While a certain anonymity provides a certain amount of freedom from consequence, the trade off for that is a lack of credibility in the eyes of those uneducated on the subject, and that's who the protesters should be trying to convince. There is no point in preaching to the choir, which is essentially what this turned into. Yes, Scientology is well known for silencing criticism, but lets not kid ourselves into thinking that they'll come into your house and slit your throat in your sleep because you showed up at some protest to smoke some herb, regardless of what you know about Operation: Freakout.
Sure, maybe some actually think they need the masks, but a fair amount of them just really want to wear that badass Guy Fawkes mask they bought a few Halloweens ago after seeing a movie about a revolutionary (with a mask modeled off of the face of a terrorist with religious motivations).
you can argue how retarded the masks, or for that matter, the entire thing is, but at least people are having the conviction to give it a go rather than just be part of the apathetic "everything's stupid" thing.
Yeah, we went over that before, and assuming that you actually leave your house to do it, I whole heartily stand behind your protest of the Church of Scientology. The masks, however, are still stupid and counter-productive.