Consider a similar scenario: climate change. Either this is a real, serious thing that needs to be dealt with, or it is a hoax. Whichever one it is, many millions of people constituting at least a large minority are wildly deluded.
There's not a ton of room for middle ground. If climate change is not real, then it is a vast power-grab on an utterly unprecedented scale that would justify any efforts to thwart it. If it is real, then the widespread belief in that power grab is a dangerous delusion.
Public policy responses do need to take everything into account, including people who believe things that are wrong. But science allows only so much flexibility there, and when the scales have been upped to the point where the alternatives are "numerous deaths" or "a vast hoax for perpetrating harm on millions", there's not a ton of room for middle ground.
Resolution is not always possible. I wish it were, but it is not. Somebody here is behaving very, very badly, and it may be more effective to simply ignore them -- assuming you can figure out which one they are. If they complain about being ignored, there's no alternative to treating it as a deadweight loss.
In my experience, even my very pro-vaccine friends eventually became more and more unsure whether the government was doing the right thing as the pandemic went on. The fact that we're debating this topic but not climate change also shows it might have more merit than it.
Also as a small-scale experiment: whenever I post these kinds of opinions my comment score does a funny dance where I can see a lot of people are up/downvoting, but the comment score basically stays at 1. That shows that HN itself is pretty split on this issue!
If you look at China, that is basically the worst nightmare of anyone who expresses doubts about how much we should trust the government to handle a pandemic. The situation is much different from ours no doubt, but it cannot be said that it's totally unreasonable to be scared of a government using a crisis to enforce authoritarian policies (what about terrorism? or drugs?).
IMO this is the same problem as the current left vs right divide in America: no one wants to concede that the other side might have a point. Instead, they'd rather make snide comments about how the other side is a bunch of children/stupid/racist/whatever, instead of understanding that other humans may have been raised different and have different opinions. There is no attempt to resolve, just overpower.