I'm not saying that it's inappropriate for HN. I flagged it because I felt the author was courting controversy and neither did he present an interesting solution. It's hard to take an unpopular side and that takes moral courage, but the extensive use of reductio ad absurdum combined with the heavy handed way he delivered his arguments made me feel that the author isn't being entirely genuine.
edit: I deleted my comment because I wasn't adding anything to the conversation either.
"Please don't submit comments complaining that a submission is inappropriate for the site. If you think something is spam or offtopic, flag it by going to its page and clicking on the "flag" link."
The site has no appropriate way for users to deal with stories they disagree with. They can flag, which cause problems as you describe, or they can make negative comments, which are supposedly the big reason HN is going downhill. Correcting individual cases will not stop this until an appropriate outlet is given to express this.
edit: I deleted my comment because I wasn't adding anything to the conversation either.