If on a site without accounts, of course each comment needs to be taken individually. But if a site has accounts and someone makes a head-scratching comment, I'll sometimes look through their post history to try to get a better understanding of the context.
If there's functionality available to view people's previous comments, then the system partly intends this to be a measure to help assess integrity and credibility, among other things.
>If we go through a users history and use it against people the only thing it does is push people to use more throwaway accounts.
What's wrong with using throwaway accounts?
>Each comment needs to stand on its own for HN to function.
I don't agree. If that's the case, then why are comments associated with usernames? Why can you see accounts' karma? That information is visible because it's intended to be visible.
Personally, I actually do tend to prefer account-less sites on average (where everything is solely a throwaway, so to speak). But if you're going to give me the tools, then I'm sometimes going to use them, especially if I suspect potential for motivated reasoning.
So I'd be happy with an anonymous HN fork. But if I'm on a non-anonymous one, I'm going to be looking at people's usernames; often reflexively. If I see something from a name I trust, it'll increase credibility for me, and if I see something from a name I distrust, it'll decrease credibility for me. And if I don't recognize it, I may look at their history and may adjust my perception based on what I see. For example, if they seem to be a "single-issue commenter".
I agree you shouldn't actually mention someone's post history in a reply unless you think it's highly, egregiously relevant. In this case, I think it's justified.