There's a difference between censorship and moderation. If I replied to your comment with vitriolic hate speech that was clearly against the community rules and the mods removed it, that would be moderation. If I merely disagreed with your ideas or expressed an unpopular opinion while staying within the rules and the mods removed it, that would be censorship. The line is admittedly fuzzy, but it's usually an issue of intent and perceived contribution to meaningful discussion.

People consciously or unconsciously associate comments with the site where they read them. This can hurt the brand of the site and be a distraction from the useful conversations that its trying to foster. Turning comments off isn't censorship, it's a matter of self-defense. It also isn't censorship by definition, as you can't censor someone without knowing what they are going to say or whether or not they are going to agree with you.

It would be nice if there was a technical solution that could separate politically divisive trolling from the informative presentation of opposing views, but that doesn't exist yet. We're left with expensive human moderation that doesn't scale well. So, for now, turning off comments is the best solution for some. Hopefully we can solve the problem by raising the overall level of public discourse, but I'd bet on a getting a technical solution to work long before that happens.