Markdown is not designed for publishing of the LaTeX class.
Here is a short treatise -- Markdown Doesn't Scale.
I liked the clearly put,
moral of the story is "use the right tool for the job", or something like that,
"even when the right tool has backslashes."
"Because if you don't, you'll just have to blog about it to admonish fellow coders - er,
document preparers - students? - people - to not make the same mistake."
Yeah, cause I made that mistake. And you shouldn't. Got it? Cool.
There is also another question here -- Markdown versus ReStructuredText
with this good point,
Markdown seems useful if you're mainly interested in generating HTML. ReStructuredText (and the related DocUtils suite) is good if you want to generate other structured output formats (eg LaTeX).
Having used both of these, I would like to have a small translator that will pickup
Markup and generate the initial LaTeX source file which can be fine tuned with more LaTeX detail.