> I see flags, especially when they are abused, as indicators that having a high-quality discussion is going to be next to impossible. If people are going to use one tool (flags) poorly, it's likely they will use a more powerful tool (comments) poorly.

Flags are the more powerful tool. A single flag is the equivalent of many upvotes and annihilates the whole discussion. That's a lot more power than a comment, which can be dealt with on an individual basis.