I'm sorry to say this, but I don't think it's fair that you (a moderator) should be allowed to pin comments to the top. There may be dozens of helpful links sharing or clarifying context in the discussion. The community can use the upvote feature to sort comments.
Exceptions might be made in cases of misinformation or abuse.
I guess for me the "pin the comment" thing is a workaround for a limitation in the software that we haven't had a chance to fix it—that is, there should be a way in the standard HN UI to associate multiple links with a story (including the archive links that many users post into the threads). Whatever mechanism we build for that, it will certainly be community-driven in the sense that users will be the ones submitting alternative links, and perhaps voting on their relevance somehow. This is related to karma too, of course.
That doesn't resolve your objection, which I think is legit. But I wanted to share why I do that.
There are other forms of pinned comment too, such as the "if you're going to comment in this thread, please make sure you're follwing the site guidelines" admonishment that I sometimes put into threads on inflammatory topics.
Exceptions might be made in cases of misinformation or abuse.