I guess the only downside is that if your client has NoScript, they just see the raw Markdown. With HTML if the client has a text based browser things like links, images, etc will still work. I still use Lynx over SSH if I need to grab paywalled content from my work machine or check something on the local intranet when I'm out of the office.

The text based browser is splitting hairs, but NoScript isn't. Unless there are browsers that will natively render Markdown if served/detected (i.e. not a plugin)?