I think a lot of people are under the assumption that Andrew Hussie wants nothing to do with Homestuck or preserving it or whatever, and that situations like this could be a slippery slope of them one day doing something else with Homestuck (I saw on reddit people are afraid this could lead to takedowns of other mirrors that host Homestuck or even paywalling Homestuck etc) But I am just not sure this whole situation is similar to the fandom takedowns of yore where the creator goes full Anne Rice and takes down whole fanfiction archives because it has her characters names in them. This does just seem like there was a personal matter we don't know about that neither of them has revealed that led to this.
But I think most people are actually just afraid of the precedent this could set. However, I will say I don't think something like that will happen because it is a bit fearmongery and also Andrew Hussie explicitly likes fanworks and has made this entire forum possible because they like fanworks. I doubt Andrew Hussie would go through the trouble of getting people licenses for homestuck and making a whole independent branch of his brand that focuses purely on fan made content if he wanted to control every single aspect of his work including fanworks.
In my opinion, Gio's second article is just a vain attempt at trying to throw suspicion onto people who have nothing to do with the actual problem at hand because he's just paranoid that anything associated with hussie is tainted and controlled by him (which just isn't true)