It is also pretty ridiculous to posit no link between the different moderation mechanisms. Being downvoted unjustly and reflexively is going to annoy commenters and make them comment back in defense. It sends a social signal that some view is unacceptable, which makes them look like troublemakers a priori.
It's also inaccurate to call this an overt feature, because there is no disclosure on affected threads. While I'm sympathetic to not wanting to stoke fires, it's fair to think the system is being gamed when I never see this happen to threads that skew in the opposite direction about a story that promotes the orthodox view. It will also create exactly the kind of unresolved discussions that guarantee a repeat until the end of time, as a self fulfilling prophecy.
The vigorous discussion should be a sign that people do want to discuss it, and I'm not convinced the flaggers and downvoters are representative of what the community at large believes. In the case of the Damore memo, informal anonymous surveys inside Google showed a very mixed landscape, in a company that skews very orthodox already. For a community that draws from a much wider geography, it is fair to assume even more disagreement. There is ample evidence of ends-justifies-means behavior from the people who want to impose their moral order on the tech scene, and pretending it isn't happening, under the guise of promoting reasonable debate, is incredibly naive.
If anything, these threads should be explicitly allowed to stand, leaving it up to individuals to decide whether to wade in, perhaps with a "keep it civil" preamble.