As a regular user, I have no interest in being witch hunted because I flagged a story. Votes and flags should be anonymous as far as other users are concerned.
It has to cost something to hide good content if you expect people to take the time to produce or submit quality content and engage with the community. Otherwise you'll end with the things no one cared much about.
This is highly irrational and speculative in nature. If an entity flags all articles by another entity or group, they should be held accountable for their actions, which could be shown to be biased. Further, a "witch hunt" would be driven by irrational decision making processes in the "hunter" aggregate, which is the point of exposing the meta data in the first place. Stopping recursive irrational thinking is the goal here.
Incorrectly indicates agreement on concensus of the aggregate. I agree with your assertions. Moderators, as infrastructure currently stands, serve an important role in shielding users from the truth of things.