Flags are worth more than upvotes - that's one of the imbalancing forces between the two. And something can be flagged off the front page (or two/three) - effectively halting any natural upvotes - without killing it.

That's true. Flags aren't downvotes. They're meant exclusively for stories that don't belong on the front page of HN, at all. Using them as a simple downvote is an abuse, and doing that routinely can get your flag power quietly revoked. Flagging helps the site much more than it hurts it, but, like everything else, it's deeply imperfect; I've had banal submissions flagged myself. The thing to do when that happens is to mail hn@yc and ask for the flags to be lifted.