In my opinion LaTeX is a poor fit for markdown, although it is the logical—and probably the only—choice. Markdown documents are supposed to be easy to read and quick to type. LaTeX is neither. When I include a matrix in my markdown document I want to type it something like:

    ## Example Matrix

    $$$
    [a, b; c, d]
    $$$

Although I realize that we are probably stuck with LaTeX for the foreseeable future as the only way to type math in text files.

Disclaimer, I am an author of an alternative math markup language specifically designed to be a good fit in Markdown.