Oswald was the assassin of JFK. The facts and evidence prove this beyond any doubt. We are 50 plus years down the road and there is no credible evidence of the involvement of any other person. At best CTers now nitpick the evidence against Oswald or attempt to apply an impossible standard of proof to imply false doubt. It is weak sauce. Just because these are vocal nuts doesn't mean that the 6th floor should entertain their baseless fantasy or be neutral about Oswald's guilt. He is not the "alleged" assassin of JFK anymore that John Wilkes Booth is the "alleged" assassin of Lincoln.
Your problem - and ours - is that most Americans disagree with this (our) view about the assassination. The 6th floor museum just can't ignore this fact. We can lament it, curse it, scream about it but that doesn't make it go away. They need to consider this fact and include it in their exhibits.
There's an increasing desire in the US at this time to suppress dissenting views. We see it all around as mostly the liberal/left is joining up with corporations to stifle views they don't like. And we know about academia. I don't like some of these views either - e.g., the election wasn't stolen from Trump and Trump didn't steal the election in 2016 - but the answer to bad speech is indeed more speech. The alternatives simply don't work.
As with the 6th Floor Museum, the response to conspiracy theories is not to ignore them but answer them with more speech. After all, isn't that what we're trying to do here? I used to be a conspiracy believer (the single bullet explanation didn't make sense but I was misled) and over time changed my mind. I can't point to an article or a book that did this; but it's clear that the more "speech" on the assassination I was exposed to made me change my mind. That's how it works.