That doesn't work too well when writing for a conference or journal with a predefined template and style file. The obvious solution -- do all your writing in Markdown and then integrate at the very end of the workflow -- doesn't work too well because you can't tell how long the document is until you use the real template.

Same goes for org-mode's Latex export.

Actually, it is acceptably straightforward to include a custom header in org-mode. Basically you can create your own latex class in customize-group org-export-latex and then add a

#+LATEX-HEADER: \input{stuff.tex}

to your file to include the appropriate header magick. I'm currently using this approach to prepare my thesis in org-mode.

Pandoc (http://johnmacfarlane.net/pandoc/) is also very good, allowing you to embed LaTeX inside markdown. So you might do

    The greek for the letter _A_ is $\alpha$

mashing up the simple markup for bold, italic, lists, headers, and quotes from markdown with the more fully-featured LaTeX support for equations.