Strictly speaking, that isn't the problem being solved by Markdown, either.

Remember that Daring Fireball does not have comments, so this isn't a concern. Markdown was something originally created to solve an authorial problem, not something for forum creators to use for comments.

It's flexible enough to do that, but it isn't the purpose of Markdown.

Why not? You have to protect against malicious HTML injection whether or not the user is using markdown, plain text or html, so why not let them use a carefully restricted subset of html?

While this is not wrong, markdown involves much less typing than HTML. Also, should one need to use HTML, markdown does allow one to switch between HTML and markdown.