I kind of see this as weird, especially in a democratic community. do the underpinnings of free speech not matter in a democratic community?
where would we be if our public officials could erase their (pr nightmare) public comments at will, and further silence any public comments the differ to their opinion?
"Free speech" doesn't apply on websites you don't own. Your right to free speech is inalienable if you are the legal owner/renter/operator of a given website; on others' websites, they are free to arbitrarily restrict your speech as they see fit, and it's completely in compliance with both the letter and spirit of the law and the US Constitution. The only other place where free speech is protected is public places, but privately owned and operated websites are not considered to legally be public places.
Second, SE communities aren't "democratic". Decisions about how to operate the communities are not made based on votes. Communities do not govern themselves by vote. SE employees, and to a lesser extent diamond mods, set the policies. Community members can influence policy if they bring up good points and manage to convince the powers that be to change policy, but no amount of upvotes is "binding". Even if your idea got 10,000 upvotes on Meta, SE would be under absolutely no obligation to implement it.
The only thing that's in any way even tangentially democratic is the process for determining the best quality or most interesting questions and answers on the site. This process is democratic in the sense that the best answer to a question is usually considered to be the one with the most upvotes, especially if it's got more votes by a wide margin. But this is merely an indicator; the results of such a vote do not compel anyone to take any particular action. Indeed, the clueful sometimes find value in less-upvoted answers, and sometimes the most-upvoted answer is objectively worse than others.
Third, comments are ephemeral. That means they can be deleted at any time, for any reason. Don't post anything as a comment that you wouldn't want to see magically disappear at any instant. The only entities that are somewhat protected from deletion on the site are questions and answers. These are only deleted if they're: (1) Spam; (2) Extremely low quality / low-effort; (3) Get a highly negative vote score and are some sort of misinformation that could lead users astray or cause them to do something harmful.
Even with questions and answers, you still don't have a "right to free speech" on SE, but the questions and answers themselves will remain on the site as long as they contribute some value (and do not mislead or possibly harm the reader) and are on-topic to the site. They are not ephemeral.
The comparison to public officials makes no sense, because SE is not a political forum. Your real life is not governed by decisions made on SE. Aside from reading false/harmful content (which is quickly identified and deleted by the community), the only negative thing that can come to you from not reading SE is ignorance of information you otherwise would've gained by participating in or reading the site.
You can't pay more taxes as a result of a decision by a moderator or SE employee. You can't lose your house, or get put in jail, or be censured or have any rights infringed on. The rights you're guaranteed do not have to be provided by SE, the moderators, or the community on SE's website.
So, yes, this is a form of censorship, but no it's not a bad form of censorship. Deleting comments that were the result of a misunderstanding is a net-positive for the community in the judgment of many moderators, because it de-escalates an issue and removes the possibility for others to get involved now or in the future and further fuel a disagreement. And it's SE's (and by extension, moderators') sole discretion to do this on their website. If you find this to be stifling, you're free to post your own opinions on a site you own, or on another site that will allow such.