Pandoc is really awesome. Even mathematics papers can be written in (mostly) markdown, and then converted to latex before compiling to PDF.

For mathematics I would also recommend using Unicode symbols in place of LaTeX commands, which makes the source even more readable. For instance

$∏_{x∈X} ∑_{y∈Y} Ψ(x,y) → ∑_{f : X → Y} ∏_{x∈Y} Ψ(x,y)$

instead of

$\prod_{x \in X} \sum_{y \in Y} \Psi(x,y) \to \sum_{f : X \to Y} \prod_{x \in Y} \Psi(x,y)$

To get this compiling, your template will have to include declarations for these such as:

\DeclareUnicodeCharacter{220F}{\ensuremath{\prod}}