Is Madoko a SAAS app? If so I'll note another problem - madoko.net is currently timing out when I go to access it; any data inside is stuck there for the duration.

On the Markdown+LaTeX note, I wrote my own Markdown parser (https://github.com/etherealmachine/markdown) to drive my github.io site (https://etherealmachine.github.io). Basically it's what you describe - easy mixing of Markdown+LaTeX to construct nice looking HTML.