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That's, sadly, the nature of humans, not the nature of a social network.
Your instance is a good example. Beehaw defederated from sh.itjust.works already, not because the admins or how they run the site are bad, but because they had open sign-ups. They were able to accept a lot of new users, and they did. Initially, this wasn't a problem, until it became clear a lot of those users were trolls. Once again, that's not necessarily the fault of the admins and Beehaw are in talks with them to refederate, but also argue that they need better moderation tools from Lemmy itself before that can happen.
Long story short is, some folks now view accounts from places like sh.itjust.works as potential trolls. Does that mean they are? No, but it does mean in a lot of users minds, that seed has been planted and they might be more skeptical of you because of that.
If you want to obscure your home instance some more, I suggest using a "Display Name" in your settings, because that will at least obfuscate your home instance in comments. People will still see your instance if they look at your full profile, but they will have to make that extra click to see where you're from.
Another, less ideal, option is to make a secondary account on an instance that has less baggage behind it, and post from there if you're worried that people will judge you for your home instance.
Personally I have no issues with anyone from sh.itjust.works and I believe them when they are trying to handle their troll problem. It's not justified to assume everyone is a bad faith actor from there. I'm just using sh.itjust.works as an example of how that might be an issue, to show I understand your concern and agree.
I think there will likely be more changes to the Lemmy codebase over time to account for things like this. Or I hope so anyway.