I would suggest that if you don't like the flag feature, you might create, or modify a Greasemonkey script to remove it locally. Greasemonkey is perfect for this sort of application- You're removing an entirely static element from the rendered page.

http://userscripts.org/scripts/search?q=ycombinator

I love HN because it is simple. Now there are too many things separated by '|'. It's less usable.